WO2008137406A1 - Method for the production of isobutanol - Google Patents

Method for the production of isobutanol Download PDF

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Publication number
WO2008137406A1
WO2008137406A1 PCT/US2008/061861 US2008061861W WO2008137406A1 WO 2008137406 A1 WO2008137406 A1 WO 2008137406A1 US 2008061861 W US2008061861 W US 2008061861W WO 2008137406 A1 WO2008137406 A1 WO 2008137406A1
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WIPO (PCT)
Prior art keywords
seq
isobutanol
gene
kivd
coli
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PCT/US2008/061861
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French (fr)
Inventor
Michael G. Bramucci
Dennis Flint
Edward S. Miller, Jr.
Vasantha Nagarajan
Natalia Sedkova
Manjari Singh
Tina K. Van Dyk
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E. I. Du Pont De Nemours And Company
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Application filed by E. I. Du Pont De Nemours And Company filed Critical E. I. Du Pont De Nemours And Company
Priority to CA002684860A priority Critical patent/CA2684860A1/en
Priority to EP08780577A priority patent/EP2140017B1/en
Priority to BRPI0809771-2A priority patent/BRPI0809771A2/en
Priority to ES08780577T priority patent/ES2399943T3/en
Publication of WO2008137406A1 publication Critical patent/WO2008137406A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/02—Preparation of oxygen-containing organic compounds containing a hydroxy group
    • C12P7/04—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic
    • C12P7/16—Butanols
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0006—Oxidoreductases (1.) acting on CH-OH groups as donors (1.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1022—Transferases (2.) transferring aldehyde or ketonic groups (2.2)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1096—Transferases (2.) transferring nitrogenous groups (2.6)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/88—Lyases (4.)
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02E—REDUCTION OF GREENHOUSE GAS [GHG] EMISSIONS, RELATED TO ENERGY GENERATION, TRANSMISSION OR DISTRIBUTION
    • Y02E50/00—Technologies for the production of fuel of non-fossil origin
    • Y02E50/10—Biofuels, e.g. bio-diesel

Definitions

  • the invention relates to a method for the production of isobutanol by fermentation using a recombinant microbial host. Specifically, the method employs a decrease in temperature during fermentation that results in more robust tolerance of the production host to the isobutanol product. BACKGROUND OF THE INVENTION
  • Butanol is an important industrial chemical, useful as a fuel additive, as a feedstock chemical in the plastics industry, and as a foodgrade extractant in the food and flavor industry. Each year 10 to12 billion pounds of butanol are produced by petrochemical means and the need for this commodity chemical will likely increase.
  • Isobutanol is produced biologically as a by-product of yeast fermentation. It is a component of "fusel oil” that forms as a result of incomplete metabolism of amino acids by this group of fungi. Isobutanol is specifically produced from catabolism of L-valine. After the amine group of L-valine is harvested as a nitrogen source, the resulting ⁇ -keto acid is decarboxylated and reduced to isobutanol by enzymes of the so-called Ehrlich pathway (Dickinson et al., J. Biol. Chem. 273(40):25752-25756 (1998)). Yields of fusel oil and/or its components achieved during beverage fermentation are typically low.
  • the concentration of isobutanol produced in beer fermentation is reported to be less than 16 parts per million (Garcia et al., Process Biochemistry 29:303-309 (1994)).
  • Addition of exogenous L-valine to the fermentation increases the yield of isobutanol, as described by Dickinson et al., supra, wherein it is reported that a yield of isobutanol of 3 g/L is obtained by providing L-valine at a concentration of 20 g/L in the fermentation.
  • the use of valine as a feed-stock would be cost prohibitive for industrial scale isobutanol production.
  • the biosynthesis of isobutanol directly from sugars would be economically viable and would represent an advance in the art.
  • Harada Hakko Kyokaishi 20:155-156 (1962) discloses that the yield of 1 -butanol in acetone- butanol-ethanol (ABE) fermentation is increased from 18.4%-18.7% to 19.1 %-21.2% by lowering the temperature from 30 0 C to 28 0 C when the growth of the bacteria reaches a maximum.
  • Jones et al. (Microbiol. Rev. 50(4):484-524 (1986)) review the role of temperature in ABE fermentation.
  • the invention provides a method for the production of isobutanol by fermentation using a recombinant microbial host, which employs a decrease in temperature during fermentation that results in more robust tolerance of the production host to the isobutanol product.
  • the invention provides a method for the production of isobutanol comprising: a) providing a recombinant microbial production host which produces isobutanol; b) seeding the production host of (a) into a fermentation medium comprising a fermentable carbon substrate to create a fermentation culture; c) growing the production host in the fermentation culture at a first temperature for a first period of time; d) lowering the temperature of the fermentation culture to a second temperature; and e) incubating the production host at the second temperature of step (d) for a second period of time; whereby isobutanol is produced.
  • Figure 1 shows four different isobutanol biosynthetic pathways.
  • SEQ ID NOs:11 -38, 40-69, 72-75, 85-138, 144, 145, 147-157, 159- 176 are the nucleotide sequences of oligonucleotide cloning, screening or sequencing primers used in the Examples described herein.
  • SEQ ID NO:39 is the nucleotide sequence of the cscBKA gene cluster described in Example 20.
  • SEQ ID NO:70 is the nucleotide sequence of the glucose isomerase promoter 1.6Gl described in Example 17.
  • SEQ ID NO:71 is the nucleotide sequence of the 1.5Gl promoter described in Example 17.
  • SEQ ID NO:76 is the nucleotide sequence of the GPD promoter described in Example 21.
  • SEQ ID NO:77 is the nucleotide sequence of the CYC1 terminator described in Example 21.
  • SEQ ID NO:79 is the nucleotide sequence of the FBA promoter described in Example 21.
  • SEQ ID NO:81 is the nucleotide sequence of ADH1 promoter described in Example 21.
  • SEQW ID NO:82 is the nucleotide sequence of ADH1 terminator described in Example 21.
  • SEQ ID NO:84 is the nucleotide sequence of GPM promoter described in Example 21.
  • SEQ ID NO:139 is the amino acid sequence of sucrose hydrolase (CscA).
  • SEQ ID NO:140 is the amino acid sequence of D-fructokinase (CscK).
  • SEQ ID NO:141 is the amino acid sequence of sucrose permease (CscB).
  • SEQ ID NO:142 is the nucleotide sequence of plasmid pFP988DssPspac described in Example 24.
  • SEQ ID NO:143 is the nucleotide sequence of plasmid pFP988DssPgroE described in Example 24.
  • SEQ ID NO:146 is the nucleotide sequence of the pFP988Dss vector fragment described in Example 24.
  • SEQ ID NO:177 is the nucleotide sequence of the pFP988 integration vector described in Example 25.
  • SEQ ID NO:267 is the nucleotide sequence of plasmid pC194 described in Example 25.
  • the present invention relates to a method for the production of isobutanol using recombinant microorganisms that employs a decrease in temperature during fermentation, resulting in more robust tolerance of the production host to the isobutanol product and therefore a higher titer of isobutanol.
  • the present invention meets a number of commercial and industrial needs.
  • Butanol is an important industrial commodity chemical with a variety of applications, where its potential as a fuel or fuel additive is particularly significant. Although only a four-carbon alcohol, butanol has an energy content similar to that of gasoline and can be blended with any fossil fuel. Butanol is favored as a fuel or fuel additive as it yields only CO2 and little or no SO ⁇ or NO ⁇ when burned in the standard internal combustion engine. Additionally butanol is less corrosive than ethanol, the most preferred fuel additive to date.
  • butanol In addition to its utility as a biofuel or fuel additive, butanol has the potential of impacting hydrogen distribution problems in the emerging fuel cell industry. Fuel cells today are plagued by safety concerns associated with hydrogen transport and distribution. Butanol can be easily reformed for its hydrogen content and can be distributed through existing gas stations in the purity required for either fuel cells or vehicles. Finally the present invention produces isobutanol from plant derived carbon sources, avoiding the negative environmental impact associated with standard petrochemical processes for butanol production.
  • compositions, a mixture, process, method, article, or apparatus that comprises a list of elements is not necessarily limited to only those elements but may include other elements not expressly listed or inherent to such composition, mixture, process, method, article, or apparatus.
  • “or” refers to an inclusive or and not to an exclusive or. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).
  • invention or "present invention” as used herein is a non- limiting term and is not intended to refer to any single embodiment of the particular invention but encompasses all possible embodiments as described in the specification and the claims.
  • the term "about" modifying the quantity of an ingredient or reactant of the invention employed refers to variation in the numerical quantity that can occur, for example, through typical measuring and liquid handling procedures used for making concentrates or use solutions in the real world; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of the ingredients employed to make the compositions or carry out the methods; and the like.
  • the term “about” also encompasses amounts that differ due to different equilibrium conditions for a composition resulting from a particular initial mixture. Whether or not modified by the term “about”, the claims include equivalents to the quantities.
  • the term “about” means within 10% of the reported numerical value, preferably within 5% of the reported numerical value.
  • isobutanol biosynthetic pathway refers to an enzyme pathway to produce isobutanol.
  • acetolactate synthase and "acetolactate synthetase” are used intechangeably herein to refer to an enzyme that catalyzes the conversion of pyruvate to acetolactate and CO2.
  • Preferred acetolactate synthases are known by the EC number 2.2.1.6 9 (Enzyme Nomenclature 1992, Academic Press, San Diego).
  • Bacillus subtilis GenBank Nos: CAB15618 (SEQ ID NO:178), Z99122 (SEQ ID NO:78), NCBI (National Center for Biotechnology Information) amino acid sequence, NCBI nucleotide sequence, respectively
  • Klebsiella pneumoniae GenBank Nos: AAA25079 (SEQ ID NO:2), M73842 (SEQ ID NO:1 )
  • Lactococcus lactis GenBank Nos: AAA25161 (SEQ ID NO:180), L16975 (SEQ ID NO:179)
  • acetohydroxy acid reductoisomerase are used interchangeably herein to refer to an enzyme that catalyzes the conversion of acetolactate to 2,3- dihydroxyisovalerate using NADPH (reduced nicotinamide adenine dinucleotide phosphate) as an electron donor.
  • NADPH reduced nicotinamide adenine dinucleotide phosphate
  • Preferred acetohydroxy acid isomeroreductases are known by the EC number 1.1.1.86 and sequences are available from a vast array of microorganisms, including, but not limited to, Escherichia coli (GenBank Nos: NP_418222 (SEQ ID NO:4), NC_000913 (SEQ ID NO:3)), Saccharomyces cerevisiae (GenBank Nos: NP_013459 (SEQ ID NO:181 ), NC_001144 (SEQ ID NO:
  • Methanococcus maripaludis GenBank Nos: CAF30210 (SEQ ID NO:183), BX957220 (SEQ ID NO:182)
  • Bacillus, subtilis GenBank Nos: CAB14789 (SEQ ID NO:185), Z99118 (SEQ ID NO:184)
  • acetohydroxy acid dehydratase refers to an enzyme that catalyzes the conversion of 2,3-dihydroxyisovalerate to ⁇ -ketoisovalerate.
  • Preferred acetohydroxy acid dehydratases are known by the EC number 4.2.1.9. These enzymes are available from a vast array of microorganisms, including, but not limited to, E. coli (GenBank Nos: YP_026248 (SEQ ID NO:6), NC_000913 (SEQ ID NO:5)), S. cerevisiae (GenBank Nos: NP_012550 (SEQ ID NO:186), NC_001142 (SEQ ID NO:83)), M.
  • branched-chain ⁇ -keto acid decarboxylase refers to an enzyme that catalyzes the conversion of ⁇ -ketoisovalerate to isobutyraldehyde and CO2.
  • Preferred branched-chain ⁇ -keto acid decarboxylases are known by the EC number 4.1.1.72 and are available from a number of sources, including, but not limited to, Lactococcus lactis (GenBank Nos: AAS49166 (SEQ ID NO:193), AY548760 (SEQ ID NO:192); CAG34226 (SEQ ID NO:8), AJ746364 (SEQ ID NO:191 ),
  • branched-chain alcohol dehydrogenase refers to an enzyme that catalyzes the conversion of isobutyraldehyde to isobutanol.
  • Preferred branched-chain alcohol dehydrogenases are known by the EC number 1.1.1.265, but may also be classified under other alcohol dehydrogenases (specifically, EC 1.1.1.1 or 1.1.1.2).
  • NADH reduced nicotinamide adenine dinucleotide
  • NADPH reduced nicotinamide adenine dinucleotide
  • S. cerevisiae GenBank Nos: NP_010656 (SEQ ID NO:199), NC_001136 (SEQ ID NO:198); NP_014051 (SEQ ID NO:201 ) NC_001145 (SEQ ID NO:200)
  • E. coli GenBank Nos: NP_417484 (SEQ ID NO:10), NC_000913 (SEQ ID NO:9)
  • C C.
  • acetobutylicum GenBank Nos: NP_349892 (SEQ ID NO:203), NC_003030 (SEQ ID NO:202); NP_349891 (SEQ ID NO:204), NC_003030 (SEQ ID NO:158)).
  • branched-chain keto acid dehydrogenase refers to an enzyme that catalyzes the conversion of ⁇ -ketoisovalerate to isobutyryl- CoA (isobutyryl-coenzyme A), using NAD + (nicotinamide adenine dinucleotide) as electron acceptor.
  • NAD + nicotinamide adenine dinucleotide
  • Preferred branched-chain keto acid dehydrogenases are known by the EC number 1.2.4.4. These branched- chain keto acid dehydrogenases are comprised of four subunits and sequences from all subunits are available from a vast array of microorganisms, including, but not limited to, B.
  • subtilis GenBank Nos: CAB14336 (SEQ ID NO:206), Z99116 (SEQ ID NO:205); CAB14335 (SEQ ID NO:208), Z99116 (SEQ ID NO:207); CAB14334 (SEQ ID NO:210), Z99116 (SEQ ID NO:209); and CAB14337 (SEQ ID NO:212), Z99116 (SEQ ID NO:211 )) and Pseudomonas putida (GenBank Nos: AAA65614 (SEQ ID NO:214), M57613 (SEQ ID NO:213); AAA65615 (SEQ ID NO:216), M57613 (SEQ ID NO:215); AAA65617 (SEQ ID NO:218), M57613 (SEQ ID NO:217); and AAA65618 (SEQ ID NO:220), M57613 (SEQ ID NO:219)).
  • acylating aldehyde dehydrogenase refers to an enzyme that catalyzes the conversion of isobutyryl-CoA to isobutyraldehyde, using either NADH or NADPH as electron donor.
  • Preferred acylating aldehyde dehydrogenases are known by the EC numbers 1.2.1.10 and 1.2.1.57. These enzymes are available from multiple sources, including, but not limited to, Clostridium beijerinckii (GenBank Nos: AAD31841 (SEQ ID
  • transaminase refers to an enzyme that catalyzes the conversion of ⁇ -ketoisovalerate to L-valine, using either alanine or glutamate as amine donor.
  • Preferred transaminases are known by the EC numbers 2.6.1.42 and 2.6.1.66. These enzymes are available from a number of sources. Examples of sources for alanine-dependent enzymes include, but are not limited to, E.
  • GenBank Nos: YP_026231 (SEQ ID NO:232), NC_000913 (SEQ ID NO:231 )) and Bacillus licheniformis (GenBank Nos: YP_093743 (SEQ ID NO:234), NC_006322 (SEQ ID NO:233)).
  • sources for glutamate-dependent enzymes include, but are not limited to, E. coli (GenBank Nos: YP_026247 (SEQ ID NO:236), NC_000913 (SEQ ID NO:235)), S.
  • valine dehydrogenase refers to an enzyme that catalyzes the conversion of ⁇ -ketoisovalerate to L-valine, using NAD(P)H as electron donor and ammonia as amine donor.
  • Preferred valine dehydrogenases are known by the EC numbers 1.4.1.8 and 1.4.1.9 and are available from a number of sources, including, but not limited to, Streptomyces coelicolor (GenBank Nos: NP_628270 (SEQ ID NO:242), NC_003888 (SEQ ID NO:241 )) and B. subtilis (GenBank Nos: CAB14339 (SEQ ID NO:244), Z99116 (SEQ ID NO:243)).
  • valine decarboxylase refers to an enzyme that catalyzes the conversion of L-valine to isobutylamine and CO2.
  • Preferred valine decarboxylases are known by the EC number 4.1.1.14. These enzymes are found in Streptomycetes, such as for example, Streptomyces viridifaciens (GenBank Nos: AAN 10242 (SEQ ID NO:246), AY116644 (SEQ ID NO:245)).
  • omega transaminase refers to an enzyme that catalyzes the conversion of isobutylamine to isobutyraldehyde using a suitable amino acid as amine donor.
  • Preferred omega transaminases are known by the EC number 2.6.1.18 and are available from a number of sources, including, but not limited to, Alcaligenes denitrificans (AAP92672 (SEQ ID NO:248), AY330220 (SEQ ID NO:247)), Ralstonia eutropha (GenBank Nos: YP_294474 (SEQ ID NO:250), NC_007347 (SEQ ID NO:249)), Shewanella oneidensis (GenBank Nos: NP_719046 (SEQ ID NO:252), NC_004347 (SEQ ID NO:251 )), and P. putida (GenBank Nos: AAN66223 (SEQ ID NO:254), AE016776 (SEQ ID NO:
  • isobutyryl-CoA mutase refers to an enzyme that catalyzes the conversion of butyryl-CoA to isobutyryl-CoA. This enzyme uses coenzyme B 12 as cofactor.
  • Preferred isobutyryl-CoA mutases are known by the EC number 5.4.99.13. These enzymes are found in a number of Streptomycetes, including, but not limited to, Streptomyces cinnamonensis (GenBank Nos: AAC08713 (SEQ ID NO:256), U67612 (SEQ ID NO:255); CAB59633 (SEQ ID NO:258), AJ246005 (SEQ ID NO:257)), S.
  • a facultative anaerobe refers to a microorganism that can grow in both aerobic and anaerobic environments.
  • carbon substrate or “fermentable carbon substrate” refers to a carbon source capable of being metabolized by host organisms disclosed herein and particularly carbon sources selected from the group consisting of monosaccharides, oligosaccharides, polysaccharides, and one-carbon substrates or mixtures thereof.
  • gene refers to a nucleic acid fragment that is capable of being expressed as a specific protein, optionally including regulatory sequences preceding (5' non-coding sequences) and following (3' non- coding sequences) the coding sequence.
  • Native gene refers to a gene as found in nature with its own regulatory sequences.
  • Chimeric gene refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature.
  • Endogenous gene refers to a native gene in its natural location in the genome of an organism.
  • foreign gene or “heterologous gene” refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer.
  • Foreign genes can comprise native genes inserted into a non- native organism, or chimeric genes.
  • a "transgene” is a gene that has been introduced into the genome by a transformation procedure.
  • an "isolated nucleic acid fragment” or “isolated nucleic acid molecule” or “genetic construct” will be used interchangeably and will mean a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases.
  • An isolated nucleic acid fragment in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA or synthetic DNA.
  • a nucleic acid fragment is "hybhdizable" to another nucleic acid fragment, such as a cDNA, genomic DNA, or RNA molecule, when a single-stranded form of the nucleic acid fragment can anneal to the other nucleic acid fragment under the appropriate conditions of temperature and solution ionic strength.
  • Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, 2 nd ed., Cold Spring Harbor Laboratory: Cold Spring Harbor, NY (1989), particularly Chapter 11 and Table 11.1 therein (entirely incorporated herein by reference). The conditions of temperature and ionic strength determine the "stringency" of the hybridization.
  • Stringency conditions can be adjusted to screen for moderately similar fragments (such as homologous sequences from distantly related organisms), to highly similar fragments (such as genes that duplicate functional enzymes from closely related organisms).
  • Post-hybridization washes determine stringency conditions.
  • One set of preferred conditions uses a series of washes starting with 6X SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2X SSC, 0.5% SDS at 45 0 C for 30 min, and then repeated twice with 0.2X SSC, 0.5% SDS at 50 0 C for 30 min.
  • a more preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2X SSC, 0.5% SDS was increased to 60 0 C.
  • Another preferred set of highly stringent conditions uses two final washes in 0.1X SSC, 0.1 % SDS at 65 0 C.
  • An additional set of stringent conditions include hybridization at 0.1X SSC, 0.1 % SDS, 65 0 C and washes with 2X SSC, 0.1 % SDS followed by 0.1 X SSC, 0.1 % SDS, for example.
  • Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible.
  • the appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences.
  • the relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA.
  • the length for a hybridizable nucleic acid is at least about 10 nucleotides.
  • a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; more preferably at least about 20 nucleotides; and most preferably the length is at least about 30 nucleotides.
  • the temperature and wash solution salt concentration may be adjusted as necessary according to factors such as length of the probe.
  • a "substantial portion" of an amino acid or nucleotide sequence is that portion comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Altschul, S. F., et al., J. MoI. Biol., 215:403-410 (1993)). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene.
  • gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques).
  • short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers.
  • a "substantial portion" of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence.
  • the instant specification teaches the complete amino acid and nucleotide sequence encoding particular fungal proteins.
  • the skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above.
  • the term "complementary" is used to describe the relationship between nucleotide bases that are capable of hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine.
  • homology and “homologous” are used interchangeably herein. They refer to nucleic acid fragments wherein changes in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate gene expression or produce a certain phenotype. These terms also refer to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotides that do not substantially alter the functional properties of the resulting nucleic acid fragment relative to the initial, unmodified fragment. It is therefore understood, as those skilled in the art will appreciate, that the invention encompasses more than the specific exemplary sequences.
  • homologous nucleic acid sequences encompassed by this invention are also defined by their ability to hybridize, under moderately stringent conditions (e.g., 0.5 X SSC, 0.1 % SDS, 60 0 C) with the sequences exemplified herein, or to any portion of the nucleotide sequences disclosed herein and which are functionally equivalent to any of the nucleic acid sequences disclosed herein.
  • moderately stringent conditions e.g., 0.5 X SSC, 0.1 % SDS, 60 0 C
  • Codon degeneracy refers to the nature in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide.
  • the skilled artisan is well aware of the "codon-bias" exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.
  • identity is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences.
  • identity also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences.
  • Identity and similarity can be readily calculated by known methods, including but not limited to those described in: 1.) Computational Molecular Biology (Lesk, A. M., Ed.) Oxford University: NY (1988); 2.) Biocomputinq: Informatics and Genome Projects (Smith, D.
  • Sequence alignments and percent identity calculations may be performed using the MegAlignTM program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wl). Multiple alignment of the sequences is performed using the "Clustal method of alignment” which encompasses several varieties of the algorithm including the "Clustal V method of alignment” corresponding to the alignment method labeled Clustal V (described by Higgins and Sharp, CABIOS. 5:151 -153 (1989); Higgins, D.G. et al., Comput. Appl. Biosci., 8:189-191 (1992)) and found in the MegAlignTM program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.).
  • Clustal W method of alignment is available and corresponds to the alignment method labeled Clustal W (described by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins, D.G. et al., Comput. Appl. Biosci. 8:189-191 (1992)) and found in the MegAlignTM v6.1 program of the
  • percent identities include, but are not limited to: 24%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, or any integer percentage from 24% to 100% may be useful in describing the present invention, such as 25%, 26%, 27%, 28%, 29%, 30%, 31 %, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41 %, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%,
  • Suitable nucleic acid fragments not only have the above homologies but typically encode a polypeptide having at least 50 amino acids, preferably at least 100 amino acids, more preferably at least 150 amino acids, still more preferably at least 200 amino acids, and most preferably at least 250 amino acids.
  • sequence analysis software refers to any computer algorithm or software program that is useful for the analysis of nucleotide or amino acid sequences.
  • Sequence analysis software may be commercially available or independently developed. Typical sequence analysis software will include, but is not limited to: 1.) the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wl); 2.) BLASTP, BLASTN, BLASTX (Altschul et al., J. MoI. Biol., 215:403-410 (1990)); 3.) DNASTAR (DNASTAR, Inc.
  • coding sequence refers to a DNA sequence that codes for a specific amino acid sequence.
  • Suitable regulatory sequences refer to nucleotide sequences located upstream (5' non-coding sequences), within, or downstream (3' non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing site, effector binding site and stem-loop structure.
  • promoter refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA.
  • a coding sequence is located 3' to a promoter sequence. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters which cause a gene to be expressed in most cell types at most times are commonly referred to as "constitutive promoters". It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.
  • operably linked refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other.
  • a promoter is operably linked with a coding sequence when it is capable of effecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter).
  • Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.
  • expression refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment disclosed herein. Expression may also refer to translation of mRNA into a polypeptide.
  • transformation refers to the transfer of a nucleic acid fragment into a host organism, resulting in genetically stable inheritance.
  • Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” or “recombinant” or “transformed” organisms.
  • Plasmid and vector refer to an extra chromosomal element often carrying genes which are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA moledules.
  • Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3' untranslated sequence into a cell.
  • Transformation vector refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitates transformation of a particular host cell.
  • cognate degeneracy refers to the nature in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide.
  • the skilled artisan is well aware of the "codon-bias" exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.
  • codon-optimized refers to genes or coding regions of nucleic acid molecules for transformation of various hosts, refers to the alteration of codons in the gene or coding regions of the nucleic acid molecules to reflect the typical codon usage of the host organism without altering the polypeptide encoded by the DNA.
  • Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1989) (hereinafter "Maniatis”); and by Silhavy, T. J., Bennan, M. L.
  • Carbohydrate utilizing microorganisms employ the Embden- Meyerhof-Parnas (EMP) pathway, the Entner-Doudoroff pathway and the pentose phosphate cycle as the central, metabolic routes to provide energy and cellular precursors for growth and maintenance. These pathways have in common the intermediate glyceraldehyde-3-phosphate and, ultimately, pyruvate is formed directly or in combination with the EMP pathway. Subsequently, pyruvate is transformed to acetyl-coenzyme A (acetyl-CoA) via a variety of means. Acetyl-CoA serves as a key intermediate, for example, in generating fatty acids, amino acids and secondary metabolites.
  • EMP Embden- Meyerhof-Parnas
  • pyruvate is formed directly or in combination with the EMP pathway.
  • pyruvate is transformed to acetyl-coenzyme A (acetyl-CoA) via a variety of means.
  • the combined reactions of sugar conversion to pyruvate produce energy (e.g. adenosine-5'-triphosphate, ATP) and reducing equivalents (e.g. reduced nicotinamide adenine dinucleotide, NADH, and reduced nicotinamide adenine dinucleotide phosphate, NADPH).
  • energy e.g. adenosine-5'-triphosphate, ATP
  • reducing equivalents e.g. reduced nicotinamide adenine dinucleotide, NADH, and reduced nicotinamide adenine dinucleotide phosphate, NADPH.
  • NADH and NADPH must be recycled to their oxidized forms (NAD + and NADP + , respectively).
  • the reducing equivalents may be used to augment the energy pool; alternatively, a reduced carbon by-product may be formed.
  • isobutanol can be produced from carbohydrate sources by recombinant
  • the preferred isobutanol pathway ( Figure 1 , steps a to e), comprises the following substrate to product conversions: a) pyruvate to acetolactate, as catalyzed for example by acetolactate synthase, b) acetolactate to 2,3-dihydroxyisovalerate, as catalyzed for example by acetohydroxy acid isomeroreductase, c) 2,3-dihydroxyisovalerate to ⁇ -ketoisovalerate, as catalyzed for example by acetohydroxy acid dehydratase, d) ⁇ -ketoisovalerate to isobutyraldehyde, as catalyzed for example by a branched-chain keto acid decarboxylase, and e) isobutyraldehyde to isobutanol, as catalyzed
  • valine biosynthesis pyruvate to ⁇ - ketoisovalerate
  • valine catabolism ⁇ -ketoisovalerate to isobutanol
  • substrate specificity is a major consideration in selecting the gene sources. For this reason, the primary genes of interest for the acetolactate synthase enzyme are those from Bacillus (alsS) and Klebsiella (budB).
  • acetolactate synthases are known to participate in butanediol fermentation in these organisms and show increased affinity for pyruvate over ketobutyrate (Gollop et al., J. Bacteriol. 172(6):3444-3449 (1990); Holtzclaw et al., J. Bacteriol. 121 (3):917-922 (1975)).
  • the second and third pathway steps are catalyzed by acetohydroxy acid reductoisomerase and dehydratase, respectively.
  • These enzymes have been characterized from a number of sources, such as for example, E. coli (Chunduru et al., Biochemistry 28(2):486-493 (1989); Flint et al., J. Biol. Chem.
  • the final two steps of the preferred isobutanol pathway are known to occur in yeast, which can use valine as a nitrogen source and, in the process, secrete isobutanol.
  • ⁇ -Ketoisovalerate can be converted to isobutyraldehyde by a number of keto acid decarboxylase enzymes, such as for example pyruvate decarboxylase.
  • pyruvate decarboxylase a number of keto acid decarboxylase enzymes, such as for example pyruvate decarboxylase.
  • a decarboxylase with decreased affinity for pyruvate is desired. So far, there are two such enzymes known in the art (Smit et al., Appl. Environ. Microbiol.
  • acetolactate synthase enzymes are available from a number of sources, for example, Bacillus subtilis (GenBank Nos: CAB15618 (SEQ ID NO:178), Z99122 (SEQ ID NO:78), NCBI (National Center for Biotechnology Information) amino acid sequence, NCBI nucleotide sequence, respectively), Klebsiella pneumoniae (GenBank Nos: AAA25079 (SEQ ID NO:2), M73842 (SEQ ID NO:1 )), and Lactococcus lactis (GenBank Nos: AAA25161 (SEQ ID NO:180), L16975 (SEQ ID NO:179)).
  • Bacillus subtilis GenBank Nos: CAB15618 (SEQ ID NO:178), Z99122 (SEQ ID NO:78), NCBI (National Center for Biotechnology Information) amino acid sequence, NCBI nucleotide sequence, respectively
  • Klebsiella pneumoniae GenBank Nos: AAA25079 (SEQ ID NO:2), M73842 (SEQ ID NO:1
  • Acetolactate to 2,3-dihydroxyisovalerate is catalyzed by acetohydroxy acid isomeroreductase.
  • polypeptides having acetohydroxy acid isomeroreductase activity isolated from a variety of sources will be useful in the present invention independent of sequence homology.
  • suitable acetohydroxy acid isomeroreductase enzymes are available from a number of sources, for example, Escherichia coli (GenBank Nos: NP_418222 (SEQ ID NO:4), NC_000913 (SEQ ID NO:3)), Saccharomyces cerevisiae (GenBank Nos: NP_013459 (SEQ ID NO:181 ), NC_001144 (SEQ ID NO:80)), Methanococcus maripaludis (GenBank Nos: CAF30210 (SEQ ID NO:183), BX957220 (SEQ ID NO:182)), and Bacillus, subtilis (GenBank Nos: CAB14789 (SEQ ID NO:185), Z99118 (SEQ ID NO:184)).
  • polypeptides having acetohydroxy acid dehydratase activity isolated from a variety of sources will be useful in the present invention independent of sequence homology.
  • suitable acetohydroxy acid dehydratase enzymes are available from a number of sources, for example, E. coli (GenBank Nos: YP_026248 (SEQ ID NO:6), NC_000913 (SEQ ID NO:5)), S. cerevisiae (GenBank Nos: NP_012550 (SEQ ID NO:186), NC_001142 (SEQ ID NO:83)), M. maripaludis (GenBank Nos: CAF29874 (SEQ ID NO:188), BX957219 (SEQ ID NO:187)), and B.
  • ⁇ -ketoisovalerate to isobutyraldehyde as catalyzed for example by a branched-chain keto acid decarboxylase.
  • branched-chain keto acid decarboxylase activity isolated from a variety of sources will be useful in the present invention independent of sequence homology.
  • Lactococcus lactis (GenBank Nos: AAS49166 (SEQ ID NO:193), AY548760 (SEQ ID NO:192); CAG34226 (SEQ ID NO:8), AJ746364 (SEQ ID NO:191 ), Salmonella typhimurium (GenBank Nos: NP_461346 (SEQ ID NO:195), NC_003197 (SEQ ID NO:194)), and Clostridium acetobutylicum (GenBank Nos: NPJ49189 (SEQ ID NO:197), NC_001988 (SEQ ID NO:196)).
  • Preferred branched-chain keto acid decarboxylase enzymes are those that have at least 80% - 85% identity to SEQ ID NO:8, SEQ ID NO:193, SEQ ID NO:
  • Example of suitable branched-chain alcohol dehydrogenase enzymes are available from a number of sources, for example, S. cerevisiae (GenBank Nos: NP_010656 (SEQ ID NO:199), NC_001136 (SEQ ID NO:198); NP_014051 (SEQ ID NO:201 ) NC_001145 (SEQ ID NO:200)), E. coli (GenBank Nos: NP_417484 (SEQ ID NO:10), NC_000913 (SEQ ID NO:9)), and C.
  • S. cerevisiae GenBank Nos: NP_010656 (SEQ ID NO:199), NC_001136 (SEQ ID NO:198); NP_014051 (SEQ ID NO:201 ) NC_001145 (SEQ ID NO:200)
  • E. coli GenBank Nos: NP_417484 (SEQ ID NO:10), NC_000913 (SEQ ID NO:9)
  • C C.
  • acetobutylicum GenBank Nos: NP_349892 (SEQ ID NO:203), NC_003030 (SEQ ID NO:202); NP_349891 (SEQ ID NO:204), NC_003030 (SEQ ID NO:158)).
  • Another pathway for converting pyruvate to isobutanol comprises the following substrate to product conversions ( Figure 1 , steps a,b,c,f,g,e): a) pyruvate to acetolactate, as catalyzed for example by acetolactate synthase, b) acetolactate to 2,3-dihydroxyisovalerate, as catalyzed for example by acetohydroxy acid isomeroreductase, c) 2,3-dihydroxyisovalerate to ⁇ -ketoisovalerate, as catalyzed for example by acetohydroxy acid dehydratase, f) ⁇ -ketoisovalerate to isobutyryl-CoA, as catalyzed for example by a branched-chain keto acid dehydrogenase, g) isobutyryl-CoA to isobut
  • the first three steps in this pathway are the same as those described above.
  • the ⁇ -ketoisovalerate is converted to isobutyryl-CoA by the action of a branched-chain keto acid dehydrogenase.
  • yeast can only use valine as a nitrogen source
  • many other organisms can use valine as the carbon source as well.
  • These organisms have branched-chain keto acid dehydrogenase (Sokatch et al. J. Bacteriol. 148(2):647-652 (1981 )), which generates isobutyryl- CoA.
  • Isobutyryl-CoA may be converted to isobutyraldehyde by an acylating aldehyde dehydrogenase.
  • Dehydrogenases active with the branched-chain substrate have been described, but not cloned, in Leuconostoc and Propionibacte ⁇ um (Kazahaya et al., J. Gen. Appl. Microbiol. 18:43-55 (1972); Hosoi et al., J. Ferment. Technol. 57:418-427 (1979)).
  • acylating aldehyde dehydrogenases known to function with straight-chain acyl-CoAs i.e.
  • butyryl-CoA may also work with isobutyryl-CoA.
  • the isobutyraldehyde is then converted to isobutanol by a branched-chain alcohol dehydrogenase, as described above for the first pathway.
  • Another pathway for converting pyruvate to isobutanol comprises the following substrate to product conversions ( Figure 1 , steps a,b,c,h,i,j,e): a) pyruvate to acetolactate, as catalyzed for example by acetolactate synthase, b) acetolactate to 2,3-dihydroxyisovalerate, as catalyzed for example by acetohydroxy acid isomeroreductase, c) 2,3-dihydroxyisovalerate to ⁇ -ketoisovalerate, as catalyzed for example by acetohydroxy acid dehydratase, h) ⁇ -ketoisovalerate to valine, as catalyzed for example by valine dehydrogenase or transaminase, i) valine to isobutylamine, as catalyzed for example by valine decarboxylase, j) isobutylamine to isobuty
  • valine dehydrogenase catalyzes reductive amination and uses ammonia; K m values for ammonia are in the millimolar range (Priestly et al., Biochem J. 261 (3):853-861 (1989); Vancura et al., J. Gen. Microbiol. 134(12):3213- 3219 (1988) Zink et al., Arch. Biochem. Biophys. 99:72-77 (1962); Sekimoto et al. J.
  • Transaminases typically use either glutamate or alanine as amino donors and have been characterized from a number of organisms (Lee-Peng et al,. J. Bacteriol. 139(2):339-345 (1979); Berg et al., J. Bacteriol. 155(3): 1009-1014 (1983)).
  • An alanine-specific enzyme may be desirable, since the generation of pyruvate from this step could be coupled to the consumption of pyruvate later in the pathway when the amine group is removed (see below).
  • the next step is decarboxylation of valine, a reaction that occurs in valanimycin biosynthesis in Streptomyces (Garg et al., MoI. Microbiol. 46(2):505-517 (2002)).
  • the resulting isobutylamine may be converted to isobutyraldehyde in a pyridoxal 5'-phosphate-dependent reaction by, for example, an enzyme of the omega- aminotransferase family.
  • an enzyme from Vibrio fluvialis has demonstrated activity with isobutylamine (Shin et al., Biotechnol. Bioeng. 65(2):206-211 (1999)).
  • the fourth isobutanol biosynthetic pathway comprises the substrate to product conversions shown as steps k,g,e in Figure 1.
  • a number of organisms are known to produce butyrate and/or butanol via a butyryl-CoA intermediate (D ⁇ rre et al., FEMS Microbiol. Rev. 17(3):251-262 (1995); Abbad-Andaloussi et al., Microbiology 142(5): 1149-1158 (1996)).
  • Isobutanol production may be engineered in these organisms by addition of a mutase able to convert butyryl-CoA to isobutyryl-CoA ( Figure 1 , step k).
  • Microbial hosts for isobutanol production may be selected from bacteria, cyanobacteria, filamentous fungi and yeasts.
  • the microbial host used for isobutanol production is preferably tolerant to isobutanol so that the yield is not limited by isobutanol toxicity.
  • Microbes that are metabolically active at high titer levels of isobutanol are not well known in the art.
  • 1-butanol-tolerant mutants have been isolated from solventogenic Clostridia, little information is available concerning the butanol tolerance of other potentially useful bacterial strains. Most of the studies on the comparison of alcohol tolerance in bacteria suggest that 1 - butanol is more toxic than ethanol (de Cavalho et al., Microsc.
  • the microbial hosts selected for the production of isobutanol are preferably tolerant to isobutanol and should be able to convert carbohydrates to isobutanol.
  • the criteria for selection of suitable microbial hosts include the following: intrinsic tolerance to isobutanol, high rate of glucose utilization, availability of genetic tools for gene manipulation, and the ability to generate stable chromosomal alterations.
  • Suitable host strains with a tolerance for isobutanol may be identified by screening based on the intrinsic tolerance of the strain.
  • the intrinsic tolerance of microbes to isobutanol may be measured by determining the concentration of isobutanol that is responsible for 50% inhibition of the growth rate (IC50) when grown in a minimal medium.
  • the IC50 values may be determined using methods known in the art.
  • the microbes of interest may be grown in the presence of various amounts of isobutanol and the growth rate monitored by measuring the optical density at 600 nanometers. The doubling time may be calculated from the logarithmic part of the growth curve and used as a measure of the growth rate.
  • the concentration of isobutanol that produces 50% inhibition of growth may be determined from a graph of the percent inhibition of growth versus the isobutanol concentration.
  • the host strain should have an IC50 for isobutanol of greater than about 0.5%.
  • the microbial host for isobutanol production should also utilize glucose at a high rate. Most microbes are capable of utilizing carbohydrates.
  • the ability to genetically modify the host is essential for the production of any recombinant microorganism.
  • the mode of gene transfer technology may be by electroporation, conjugation, transduction or natural transformation.
  • a broad range of host conjugative plasmids and drug resistance markers are available.
  • the cloning vectors are tailored to the host organisms based on the nature of antibiotic resistance markers that can function in that host.
  • the microbial host also has to be manipulated in order to inactivate competing pathways for carbon flow by deleting various genes. This requires the availability of either transposons to direct inactivation or chromosomal integration vectors. Additionally, the production host should be amenable to chemical mutagenesis so that mutations to improve intrinsic isobutanol tolerance may be obtained.
  • suitable microbial hosts for the production of isobutanol include, but are not limited to, members of the genera Clostridium, Zymomonas, Escherichia, Salmonella,
  • Rhodococcus Pseudomonas, Bacillus, Lactobacillus, Enterococcus, Alcaligenes, Klebsiella, Paenibacillus, Arthrobacter, Corynebacterium, Brevibacterium, Pichia, Candida, Hansenula and Saccharomyces.
  • Preferred hosts include: Escherichia coli, Alcaligenes eutrophus, Bacillus licheniformis, Paenibacillus macerans, Rhodococcus erythropolis,
  • Recombinant organisms containing the necessary genes that will encode the enzymatic pathway for the conversion of a fermentable carbon substrate to isobutanol may be constructed using techniques well known in the art.
  • Genes encoding the enzymes of one of the isobutanol biosynthetic pathways of the invention for example, acetolactate synthase, acetohydroxy acid isomeroreductase, acetohydroxy acid dehydratase, branched-chain ⁇ -keto acid decarboxylase, and branched- chain alcohol dehydrogenase, may be isolated from various sources, as described above.
  • Vectors or cassettes useful for the transformation of a variety of host cells are common and commercially available from companies such as EPICENTRE® (Madison, Wl), Invitrogen Corp. (Carlsbad, CA),
  • the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration.
  • Suitable vectors comprise a region 5' of the gene which harbors transcriptional initiation controls and a region 3' of the DNA fragment which controls transcriptional termination. Both control regions may be derived from genes homologous to the transformed host cell, although it is to be understood that such control regions may also be derived from genes that are not native to the specific species chosen as a production host.
  • Initiation control regions or promoters which are useful to drive expression of the relevant pathway coding regions in the desired host cell are numerous and familiar to those skilled in the art.
  • Virtually any promoter capable of driving these genetic elements is suitable for the present invention including, but not limited to, CYC1, HIS3, GAL1, GAL10, ADH 1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI, CUP1, FBA, GPD, and GPM (useful for expression in Saccharomyces); A0X1 (useful for expression in Pichia); and lac, ara, tet, trp, IP L , IP R , Tl, tac, and trc (useful for expression in Escherichia coli, Alcaligenes, and
  • Pseudomonas the amy, apr, npr promoters and various phage promoters useful for expression in Bacillus subtilis, Bacillus licheniformis, and Paenibacillus macerans; nisA (useful for expression Gram-positive bacteria, Eichenbaum et al. Appl. Environ. Microbiol. 64(8):2763-2769 (1998)); and the synthetic P11 promoter (useful for expression in Lactobacillus plantarum, Rud et al., Microbiology 152:1011 -1019 (2006)).
  • Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary, however, it is most preferred if included.
  • Certain vectors are capable of replicating in a broad range of host bacteria and can be transferred by conjugation.
  • the complete and annotated sequence of pRK404 and three related vectors-pRK437, pRK442, and pRK442(H) are available. These derivatives have proven to be valuable tools for genetic manipulation in Gram-negative bacteria
  • Plasmid 50(1 ):74-79 (2003) Several plasmid derivatives of broad-host-range lnc P4 plasmid RSF1010 are also available with promoters that can function in a range of Gram-negative bacteria. Plasmid pAYC36 and pAYC37, have active promoters along with multiple cloning sites to allow for the heterologous gene expression in Gram- negative bacteria.
  • thermosensitive variant of the broad-host-range replicon pWV101 has been modified to construct a plasmid pVE6002 which can be used to effect gene replacement in a range of Gram-positive bacteria (Maguin et al., J. Bacteriol. 174(17):5633-5638 (1992)).
  • in vitro transposomes are available to create random mutations in a variety of genomes from commercial sources such as EPICENTRE ® .
  • Vectors or cassettes useful for the transformation of E. coli are common and commercially available from the companies listed above.
  • the genes of an isobutanol biosynthetic pathway may be isolated from various sources, cloned into a modified pUC19 vector and transformed into E. coli NM522, as described in Examples 10 and 11.
  • E. coli-Rhodococcus shuttle vectors are available for expression in R. erythropolis, including, but not limited to, pRhBR17 and pDA71 (Kostichka et al., Appl. Microbiol. Biotechnol. 62:61 -68(2003)).
  • Targeted gene disruption of chromosomal genes in R. erythropolis may be created using the method described by Tao et al., supra, and Brans et al. (Appl. Environ.
  • heterologous genes required for the production of isobutanol may be cloned initially in pDA71 or pRhBR71 and transformed into E. coli.
  • the vectors may then be transformed into R. erythropolis by electroporation, as described by Kostichka et al., supra.
  • the recombinants may be grown in synthetic medium containing glucose and the production of isobutanol can be followed using methods known in the art. Expression of an isobutanol biosvnthetic pathway in B. Subtilis
  • genes of an isobutanol biosynthetic pathway may be isolated from various sources, cloned into a modified pUC19 vector and transformed into Bacillus subtilis BE1010, as described in Example 12.
  • the five genes of an isobutanol biosynthetic pathway can be split into two operons for expression, as described in Example 24.
  • the three genes of the pathway (bubB, HvD, and kivD) were integrated into the chromosome of Bacillus subtilis BE101010
  • plasmids and shuttle vectors that replicate in B. subtilis may be used to transform B. licheniformis by either protoplast transformation or electroporation.
  • the genes required for the production of isobutanol may be cloned in plasmids pBE20 or pBE60 derivatives (Nagarajan et al., Gene 114:121 -126 (1992)).
  • Methods to transform B. licheniformis are known in the art (for example see Fleming et al. Appl. Environ. Microbiol., 61 (11 ):3775-3780 (1995)).
  • the plasmids constructed for expression in B. subtilis may be transformed into B. licheniformis to produce a recombinant microbial host that produces isobutanol.
  • Plasmids may be constructed as described above for expression in B. subtilis and used to transform Paenibacillus macerans by protoplast transformation to produce a recombinant microbial host that produces isobutanol.
  • Saccharomyces cerevisiae Methods for gene expression in Saccharomyces cerevisiae are known in the art (see for example Methods in Enzymology, Volume 194, Guide to Yeast Genetics and Molecular and Cell Biology (Part A, 2004, Christine Guthrie and Gerald R. Fink (Eds.), Elsevier Academic Press, San Diego, CA). Expression of genes in yeast typically requires a promoter, followed by the gene of interest, and a transcriptional terminator.
  • yeast promoters can be used in constructing expression cassettes for genes encoding an isobutanol biosynthetic pathway, including, but not limited to constitutive promoters FBA, GPD, ADH1 , and GPM, and the inducible promoters GAL1 , GAL10, and CUP1.
  • Suitable transcriptional terminators include, but are not limited to FBAt, GPDt, GPMt, ERGIOt, GALIt, CYC1 , and ADH1.
  • suitable promoters, transcriptional terminators, and the genes of an isobutanol biosynthetic pathway may be cloned into E. co//-yeast shuttle vectors as described in Example 21. Expression of an isobutanol biosvnthetic pathway in Lactobacillus plantarum
  • the Lactobacillus genus belongs to the Lactobacillales family and many plasmids and vectors used in the transformation of Bacillus subtilis and Streptococcus may be used for lactobacillus.
  • suitable vectors include pAM ⁇ i and derivatives thereof (Renault et al., Gene 183:175-182 (1996); and O'Sullivan et al., Gene 137:227-231 (1993)); pMBB1 and pHW800, a derivative of pMBB1 (Wyckoff et al. Appl. Environ. Microbiol. 62:1481-1486 (1996)); pMG1 , a conjugative plasmid (Tanimoto et al., J.
  • the Enterococcus genus belongs to the Lactobacillales family and many plasmids and vectors used in the transformation of Lactobacillus, Bacillus subtilis, and Streptococcus may be used for Enterococcus.
  • suitable vectors include pAM ⁇ i and derivatives thereof (Renault et al., Gene 183:175-182 (1996); and O'Sullivan et al., Gene 137:227-231 (1993)); pMBB1 and pHW800, a derivative of pMBB1 (Wyckoff et al. Appl. Environ. Microbiol.
  • faecalis using the nisA gene from Lactococcus may also be used (Eichenbaum et al., Appl. Environ. Microbiol. 64:2763-2769 (1998). Additionally, vectors for gene replacement in the E. faecium chromosome may be used (Nallaapareddy et al., Appl. Environ. Microbiol. 72:334-345 (2006)). For example, expression of an isobutanol biosynthetic pathway in Enterococcus faecalis is described in Example 26. Fermentation Media
  • Fermentation media in the present invention must contain suitable carbon substrates.
  • suitable substrates may include but are not limited to monosaccharides such as glucose and fructose, oligosaccharides such as lactose or sucrose, polysaccharides such as starch or cellulose or mixtures thereof and unpuhfied mixtures from renewable feedstocks such as cheese whey permeate, cornsteep liquor, sugar beet molasses, and barley malt.
  • the carbon substrate may also be one-carbon substrates such as carbon dioxide, or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated.
  • methylotrophic organisms are also known to utilize a number of other carbon containing compounds such as methylamine, glucosamine and a variety of amino acids for metabolic activity.
  • methylotrophic yeast are known to utilize the carbon from methylamine to form trehalose or glycerol (Bellion et al., Microb. Growth C1 Compd., [Int. Symp.], 7th (1993), 415-32. Editor(s): Murrell, J. CoIMn; Kelly, Don P. Publisher: Intercept, Andover, UK).
  • various species of Candida will metabolize alanine or oleic acid (Suiter et al., Arch. Microbiol. 153:485-489 (1990)).
  • the source of carbon utilized in the present invention may encompass a wide variety of carbon containing substrates and will only be limited by the choice of organism.
  • preferred carbon substrates are glucose, fructose, and sucrose.
  • Sucrose may be derived from renewable sugar sources such as sugar cane, sugar beets, cassava, sweet sorghum, and mixtures thereof.
  • Glucose and dextrose may be derived from renewable grain sources through saccharification of starch based feedstocks including grains such as corn, wheat, rye, barley, oats, and mixtures thereof.
  • fermentable sugars may be derived from renewable cellulosic or lignocellulosic biomass through processes of pretreatment and saccharification, as described, for example, in co-owned and co-pending U.S.
  • Biomass refers to any cellulosic or lignocellulosic material and includes materials comprising cellulose, and optionally further comprising hemicellulose, lignin, starch, oligosaccharides and/or monosaccharides. Biomass may also comprise additional components, such as protein and/or lipid. Biomass may be derived from a single source, or biomass can comprise a mixture derived from more than one source; for example, biomass may comprise a mixture of corn cobs and corn stover, or a mixture of grass and leaves.
  • Biomass includes, but is not limited to, bioenergy crops, agricultural residues, municipal solid waste, industrial solid waste, sludge from paper manufacture, yard waste, wood and forestry waste.
  • biomass include, but are not limited to, corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat, wheat straw, barley, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, soy, components obtained from milling of grains, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof.
  • fermentation media In addition to an appropriate carbon source, fermentation media must contain suitable minerals, salts, cofactors, buffers and other components, known to those skilled in the art, suitable for the growth of the cultures and promotion of the enzymatic pathway necessary for isobutanol production.
  • the recombinant microbial production host which produces isobutanol is seeded into a fermentation medium comprising a fermentable carbon substrate to create a fermentation culture.
  • the production host is grown in the fermentation culture at a first temperature for a first period of time.
  • the first temperature is typically from about 25 0 C to about 40 0 C.
  • Suitable fermentation media in the present invention include common commercially prepared media such as Luria Bertani (LB) broth, Sabouraud Dextrose (SD) broth or Yeast Medium (YM) broth.
  • Other defined or synthetic growth media may also be used, and the appropriate medium for growth of the particular microorganism will be known by one skilled in the art of microbiology or fermentation science.
  • agents known to modulate catabolite repression directly or indirectly e.g., cyclic adenosine 2':3'-monophosphate, may also be incorporated into the fermentation medium.
  • Suitable pH ranges for the fermentation are between pH 5.0 to pH 9.0, where pH 6.0 to pH 8.0 is preferred as the initial condition.
  • Fermentations may be performed under aerobic or anaerobic conditions, where anaerobic or microaerobic conditions are preferred.
  • the first period of time to grow the production host at the first temperature may be determined in a variety of ways. For example, during this period of growth a metabolic parameter of the fermentation culture may be monitored.
  • the metabolic parameter that is monitored may be any parameter known in the art, including, but not limited to the optical density, pH, respiratory quotient, fermentable carbon substrate utilization, CO2 production, and isobutanol production.
  • additional fermentable carbon substrate may be added, the pH may be adjusted, oxygen may be added for aerobic cells, or other culture parameters may be adjusted to support the metabolic activity of the culture.
  • a decrease in metabolic activity may be indicated by a decrease in one or more of the following parameters: rate of optical density change, rate of pH change, rate of change in respiratory quotient (if the host cells are aerobic), rate of fermentable carbon substrate utilization, rate of isobutanol production, rate of change in CO 2 production, or rate of another metabolic parameter.
  • rate of optical density change if the host cells are aerobic
  • rate of fermentable carbon substrate utilization if the host cells are aerobic
  • rate of isobutanol production rate of change in CO 2 production
  • rate of another metabolic parameter rate of another metabolic parameter.
  • the decrease in metabolic activity is related to the sensitivity of the host cells to the production of isobutanol and/or the presence of isobutanol in the culture.
  • the temperature of the fermentation culture is lowered to reduce the sensitivity of the host cells to isobutanol and thereby allow further production of isobutanol.
  • the lowering of the temperature coincides with a change in the metabolic parameter that is monitored.
  • the change in metabolic activity is a decrease in the rate of isobutanol production.
  • Isobutanol production may be monitored by analyzing the amount of isobutanol present in the fermentation culture medium as a function of time using methods well known in the art, such as using high performance liquid chromatography (HPLC) or gas chromatography (GC), which are described in the Examples herein. GC is preferred due to the short assay time.
  • HPLC high performance liquid chromatography
  • GC gas chromatography
  • the lowering of the temperature of the fermentation culture may occur at a predetermined time.
  • the first period of time may be predetermined by establishing a correlation between a metabolic parameter of the fermentation culture and time in a series of test fermentations runs.
  • a correlation between a metabolic parameter, as described above, and time of culture growth may be established for any isobutanol producing host by one skilled in the art.
  • the specific correlation may vary depending on conditions used including, but not limited to, carbon substrate, fermentation conditions, and the specific recombinant isobutanol producing microbial production host.
  • the correlation is most suitably made between isobutanol production or specific glucose consumption rate and time of culture growth.
  • the temperature in subsequent fermentations runs is lowered after 12 hours without the need to monitor isobutanol production in the subsequent runs.
  • the temperature of the fermentation culture is lowered to a second temperature.
  • the second temperature is about 3 0 C to about 25 0 C lower than the first temperature. Reduction in temperature to enhance tolerance of the host cells to isobutanol is balanced with maintaining the temperature at a level where the cells continue to be metabolically active for isobutanol production.
  • a fermentation culture that has been grown at about 35 0 C may be reduced in temperature to about 28 0 C; or a culture grown at about 30 0 C may be reduced in temperature to about 25 0 C.
  • the change in temperature may be done gradually over time or may be made as a step change.
  • the production host is incubated at the second temperature for a second period of time, so that isobutanol production continues.
  • the second period of time may be determined in the same manner as the first period of time described above, e.g., by monitoring a metabolic parameter or by using a predetermined time.
  • the temperature lowering and incubation steps may be repeated one or more times to more finely balance metabolic activity for isobutanol production and isobutanol sensitivity.
  • a culture that has been grown at about 35 0 C may be reduced in temperature to about 32 0 C, followed by an incubation period.
  • a metabolic parameter of the fermentation culture may be monitored as described above, or a predetermined time may be used. It is particularly suitable to monitor the production of isobutanol during this incubation period.
  • the temperature may be reduced a second time. For example, the temperature may be reduced from about 32 0 C to about 28 0 C.
  • the temperature lowering and incubation steps may be repeated a third time where the temperature is reduced, for example, to about 20 0 C.
  • the production host is incubated at the lowered temperature so that isobutanol production continues. The steps may be repeated further as necessary to obtain the desired isobutanol titer.
  • the present process employs a batch method of fermentation.
  • a classical batch fermentation is a closed system where the composition of the medium is set at the beginning of the fermentation and not subject to artificial alterations during the fermentation. Thus, at the beginning of the fermentation the medium is inoculated with the desired organism or organisms, and fermentation is permitted to occur without adding anything to the system.
  • a "batch" fermentation is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration.
  • the metabolite and biomass compositions of the system change constantly up to the time the fermentation is stopped.
  • Within batch cultures cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted.
  • Fed-Batch fermentation processes are also suitable in the present invention and comprise a typical batch system with the exception that the substrate is added in increments as the fermentation progresses.
  • Fed-Batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO 2 .
  • Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth.
  • Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration.
  • one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate.
  • a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant.
  • Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to the medium being drawn off must be balanced against the cell growth rate in the fermentation.
  • the present invention may be practiced using either batch, fed-batch or continuous processes and that any known mode of fermentation would be suitable. Additionally, it is contemplated that cells may be immobilized on a substrate as whole cell catalysts and subjected to fermentation conditions for isobutanol production. Methods for lsobutanol Isolation from the Fermentation Medium
  • the bioproduced isobutanol may be isolated from the fermentation medium using methods known in the art. For example, solids may be removed from the fermentation medium by centrifugation, filtration, decantation, or the like. Then, the isobutanol may be isolated from the fermentation medium, which has been treated to remove solids as described above, using methods such as distillation, liquid-liquid extraction, or membrane-based separation. Because isobutanol forms a low boiling point, azeotropic mixture with water, distillation can only be used to separate the mixture up to its azeotropic composition. Distillation may be used in combination with another separation method to obtain separation around the azeotrope.
  • isobutanol may be isolated using azeotropic distillation using an entrainer (see for example Doherty and Malone, Conceptual Design of Distillation Systems, McGraw Hill, New York, 2001 ).
  • the isobutanol-water mixture forms a heterogeneous azeotrope so that distillation may be used in combination with decantation to isolate and purify the isobutanol.
  • the isobutanol containing fermentation broth is distilled to near the azeotropic composition.
  • the azeotropic mixture is condensed, and the isobutanol is separated from the fermentation medium by decantation.
  • the decanted aqueous phase may be returned to the first distillation column as reflux.
  • the isobutanol- rich decanted organic phase may be further purified by distillation in a second distillation column.
  • the isobutanol may also be isolated from the fermentation medium using liquid-liquid extraction in combination with distillation.
  • the isobutanol is extracted from the fermentation broth using liquid-liquid extraction with a suitable solvent.
  • the isobutanol-containing organic phase is then distilled to separate the isobutanol from the solvent.
  • Distillation in combination with adsorption may also be used to isolate isobutanol from the fermentation medium.
  • the fermentation broth containing the isobutanol is distilled to near the azeotropic composition and then the remaining water is removed by use of an adsorbent, such as molecular sieves (Aden et al. Lignocellulosic
  • distillation in combination with pervaporation may be used to isolate and purify the isobutanol from the fermentation medium.
  • the fermentation broth containing the isobutanol is distilled to near the azeotropic composition, and then the remaining water is removed by pervaporation through a hydrophilic membrane (Guo et al., J. Membr. Sci. 245, 199-210 (2004)).
  • Microbial strains were obtained from The American Type Culture Collection (ATCC), Manassas, VA, unless otherwise noted.
  • oligonucleotide primers to use in the following Examples are given in Table 4. All the oligonucleotide primers are synthesized by Sigma-Genosys (Woodlands, TX).
  • the concentration of isobutanol in the culture media can be determined by a number of methods known in the art.
  • HPLC high performance liquid chromatography
  • a specific high performance liquid chromatography (HPLC) method utilized a Shodex SH-1011 column with a Shodex SH-G guard column, both purchased from Waters Corporation (Milford, MA), with refractive index (Rl) detection. Chromatographic separation was achieved using 0.01 M H 2 SO 4 as the mobile phase with a flow rate of 0.5 mL/min and a column temperature of 50 0 C. Isobutanol had a retention time of 46.6 min under the conditions used.
  • gas chromatography (GC) methods are available.
  • a specific GC method utilized an HP-INNOWax column (30 m x 0.53 mm id,1 ⁇ m film thickness, Agilent Technologies, Wilmington, DE), with a flame ionization detector (FID).
  • the carrier gas was helium at a flow rate of 4.5 mL/min, measured at 150 0 C with constant head pressure; injector split was 1 :25 at 200 0 C; oven temperature was 45 0C for 1 min, 45 to 220 0 C at 10 °C/min, and 220 0 C for 5 min; and FID detection was employed at 240 0 C with 26 mL/min helium makeup gas.
  • the retention time of isobutanol was 4.5 min.
  • EXAMPLE 1 Increased tolerance of Lactobacillus plantarum PN0512 to 1 -butanol, iso- butanol and 2-butanol at decreased growth temperatures
  • Tolerance levels of bacterial strain Lactobacillus plantarum PN0512 were determined at 25 0 C, 30 0 C and 37 0 C as follows.
  • the strain was cultured in S30L medium (i.e., 10 mM ammonium sulfate, 5 mM potassium phosphate buffer, pH 7.0, 50 mM MOPS, pH 7.0, 2 mM MgCI 2 , 0.7 mM CaCI 2 , 50 ⁇ M MnCI 2 , 1 ⁇ M FeCI 3 , 1 ⁇ M ZnCI 2 , 1.72 ⁇ M CuCI 2 , 2.53 ⁇ M CoCI 2 , 2.42 ⁇ M Na 2 MoO 4 , 2 ⁇ M thiamine hydrochloride, 10 mM glucose, and 0.2% yeast extract).
  • S30L medium i.e., 10 mM ammonium sulfate, 5 mM potassium phosphate buffer, pH 7.0, 50 mM MOPS, pH 7.0, 2 m
  • the 1 - butanol exposure at 0 0 C was done after allowing the overnight cultures to cool on ice for about 15 min.
  • a series of solutions of 1 -butanol at different concentrations in LB medium was made and 90 ⁇ L aliquots were put in microfuge tubes. To these were added 10 ⁇ L of the overnight cultures and the tubes were immediately placed in shaking incubators at 42 0 C or 28 0 C or left on ice for 30 min.
  • a 10 ⁇ 2 dilution was done by placing 2 ⁇ L of the treated culture into 198 ⁇ L of LB medium in wells of a microplate.
  • E. coli strain MG1655 was allowed to grow overnight in MOPS 0.2% glucose medium (Teknova, Half Moon Bay, CA) at 42 0 C or 28 0 C. The following day, the cultures were diluted into fresh medium and allowed to grow at the same temperature until in the log phase of growth.
  • the OD600 was 0.74 for the 28 0 C culture and was 0.72 for the 42 0 C culture. Both of these log phase cultures were exposed to 1 -butanol at 42 0C, 28 0 C and 0 0 C as follows. A series of solutions of 1 -butanol at different concentrations in MOPS 0.2% glucose medium was made and 90 ⁇ l_ aliquots were put in microfuge tubes. To these were added 10 ⁇ L of the log phase cultures and the tubes were immediately placed in shaking incubators at 42 0 C or 28 0 C or left on ice for 30 min.
  • a 10 2 dilution was done by placing 2 ⁇ L of the treated culture into 198 ⁇ L of LB medium in wells of a microplate. Then 5 ⁇ l_ of the undiluted treated cultures were spotted on LB agar plates. Subsequent 10-fold serial dilutions of 10 ⁇ 3 , 10 ⁇ 4 , 10 ⁇ 5 and 10 ⁇ 6 of the exposed cultures were done by serial pipetting of 20 ⁇ l_, starting with the 10 ⁇ 2 dilution cultures, into 180 ⁇ l_ of LB medium in the microplate, using a multi-channel pipette. Prior to each transfer, the cultures were mixed by pipetting up and down six times.
  • E. coli strain BW25113 The Coli Genetic Stock Center (CGSC), Yale University; # 7636
  • LB medium Teknova, Half Moon Bay, CA
  • MEK shock was tested at exposure temperatures of 28 0 C or 37 0 C.
  • a series of solutions of MEK at different concentrations in LB medium was made and 90 ⁇ L aliquots were put in microfuge tubes.
  • EXAMPLE 4 Increased tolerance of E. coli and L plantarum PN0512 to 1 -Butanol at decreased exposure temperature This Example demonstrates that the toxic effects of 1 -butanol and
  • E. coli - Miller's LB medium (Teknova, Half Moon Bay, CA): L. plantarum PN0512 - Lactobacilli MRS Broth (BD Diagnostics
  • the E. coli and L. plantarum cultures were grown at 37 0 C aerobically with shaking until the cultures were in log phase and the OD600 was between 0.6 and 0.8.
  • a 50 ⁇ l_ aliquot of each culture was removed for a time zero sample.
  • the remainder of the cultures was divided into six 5 ml_ portions and placed in six small incubation flasks or tubes. Different amounts of 1 - butanol or 2-butanol were added to the six flasks to bring the concentration to predetermined values, as listed in the tables below.
  • the flasks or tubes were incubated at a desired temperature, aerobically without shaking for 1 h.
  • the 10 ⁇ 3 dilution was prepared by pipetting 20 ⁇ l_ of the sample from the head well into the 180 ⁇ l_ LB medium in the next well using a multi- channel pipette. This procedure was repeated 3 more times on successive wells to prepare the 10 ⁇ 4 , 10 ⁇ 5 , and 10 ⁇ 6 dilutions. After each liquid transfer, the solution in the well was mixed by pipetting it up and down 10 times with the multi-channel pipetor. A 5 ⁇ L aliquot of each dilution was spotted onto an LB plate using a multi-channel pipette starting with the 10 ⁇ 6 dilution, then the 10 ⁇ 5 , and so on working from more to less dilute without a change of tips.
  • the spots were allowed to soak into the agar by leaving the lid of the plate slightly open for 15 to 30 min in a sterile transfer hood.
  • the plates were covered, inverted, and incubated overnight at 37 0 C. The following day, the number of colonies in the spots were counted from the different dilutions.
  • the number of living cells/mL in each of the original culture solutions from which the 2 ⁇ L was withdrawn was calculated and compared to the number of cells in the control untreated culture to determine the % of the cells surviving.
  • the concentration at which 1 -butanol kills E. coli cells was affected by the treatment temperature. At 0 0 C, concentrations of 1-butanol as high as 4.5% v/v had no toxic effect on E. coli cells during a one hour treatment. At 30 0 C, E. coli cells were killed when treated with 3% v/v 1 - butanol for one hour. At 37 0 C, E. coli cells were killed when treated with 2% v/v 1 -butanol for one hour.
  • the concentration at which 1 -butanol kills L. plantarum PN0512 cells was affected by the treatment temperature. At 0 0 C, concentrations of 1 -butanol as high as 4.5% v/v had no toxic effect on L. plantarum PN0512 cells during a one hour treatment. At 23 0 C, L. plantarum PN0512 cells were killed when treated with 3.5% v/v 1 -butanol for one hour. At 37 0 C, L. plantarum PN0512 cells were killed when treated with 2.5 % v/v 1 -butanol for one hour.
  • the purpose of this Example was to clone the budB gene from Klebsiella pneumoniae and express it in E. coli BL21 -AI.
  • the budB gene was amplified from Klebsiella pneumoniae strain ATCC 25955 genomic DNA using PCR, resulting in a 1.8 kbp product.
  • Genomic DNA was prepared using the Gentra Puregene kit (Gentra Systems, Inc., Minneapolis, MN; catalog number D-5000A).
  • Gentra Puregene kit Gentra Systems, Inc., Minneapolis, MN; catalog number D-5000A.
  • the budB gene was amplified from Klebsiella pneumoniae genomic DNA by PCR using primers N80 and N81 (see Table 2), given as SEQ ID NOs:11 and 12, respectively.
  • Other PCR amplification reagents were supplied in manufacturers' kits, for example, Finnzymes PhusionTM High-Fidelity PCR Master Mix (New England Biolabs Inc., Beverly, MA; catalog no. F-531 ) and used according to the manufacturer's protocol.
  • Amplification was carried out in a DNA Thermocycler GeneAmp 9700 (PE Applied Biosystems, Foster city, CA).
  • the entry vector pENTRSDD-TOPO allowed directional cloning and provided a Shine-Dalgarno sequence for the gene of interest.
  • the destination vector pDEST14 used a T7 promoter for expression of the gene with no tag.
  • the forward primer incorporated four bases (CACC) immediately adjacent to the translational start codon to allow directional cloning into pENTRSDD-TOPO (Invitrogen) to generate the plasmid pENTRSDD-TOPObudB.
  • CACC cACC
  • the pENTR construct was transformed into E. coli Top10 (Invitrogen) cells and plated according to manufacturer's recommendations.
  • Transformants were grown overnight and plasmid DNA was prepared using the QIAprep Spin Miniprep kit (Qiagen, Valencia, CA; catalog no. 27106) according to manufacturer's recommendations. Clones were sequenced to confirm that the genes inserted in the correct orientation and to confirm the sequence.
  • the nucleotide sequence of the open reading frame (ORF) for this gene and the predicted amino acid sequence of the enzyme are given as SEQ ID NO:1 and SEQ ID NO:2, respectively.
  • the budB gene was transferred to the pDEST 14 vector by recombination to generate pDEST14budB.
  • the pDEST14budB vector was transformed into E. coli BL21 -AI cells (Invitrogen). Transformants were inoculated into Luria Bertani (LB) medium supplemented with 50 ⁇ g/mL of ampicillin and grown overnight. An aliquot of the overnight culture was used to inoculate 50 ml_ of LB supplemented with 50 ⁇ g/mL of ampicillin. The culture was incubated at 37 0 C with shaking until the OD 6 oo reached 0.6-0.8.
  • the culture was split into two 25-mL cultures and arabinose was added to one of the flasks to a final concentration of 0.2% w/v.
  • the negative control flask was not induced with arabinose.
  • the flasks were incubated for 4 h at 37 0 C with shaking. Cells were harvested by centhfugation and the cell pellets were resuspended in 50 mM MOPS, pH 7.0 buffer. The cells were disrupted either by sonication or by passage through a French Pressure Cell. The whole cell lysate was centrifuged yielding the supernatant or cell free extract and the pellet or the insoluble fraction.
  • Example 6 (Prophetic) Cloning and Expression of Acetohvdroxy Acid Reductoisomerase The purpose of this prophetic Example is to describe how to clone the HvC gene from E. coli K12 and express it in E. coli BL21 -AI.
  • the HvC gene is amplified from E. coli genomic DNA using PCR.
  • the HvC gene is cloned and expressed in the same manner as the budB gene described in Example 5.
  • Genomic DNA from E. coli is prepared using the Gentra Puregene kit (Gentra Systems, Inc.,
  • the HvC gene is amplified by PCR using primers N100 and N101 (see Table 2), given as SEQ ID NOs: 13 and 14, respectively, creating a 1.5 kbp product.
  • the forward primer incorporates four bases (CCAC) immediately adjacent to the translational start codon to allow directional cloning into pENTR/SD/D- TOPO (Invitrogen) to generate the plasmid pENTRSDD-TOPOilvC.
  • Clones are sequenced to confirm that the genes are inserted in the correct orientation and to confirm the sequence.
  • the nucleotide sequence of the open reading frame (ORF) for this gene and the predicted amino acid sequence of the enzyme are given as SEQ ID NO:3 and SEQ ID NO:4, respectively.
  • the HvC gene is transferred to the pDEST 14 (Invitrogen) vector by recombination to generate pDEST14ilvC.
  • the pDEST14ilvC vector is transformed into E. coli BL21 -AI cells and expression from the T7 promoter is induced by addition of arabinose.
  • a protein of the expected molecular weight of about 54 kDa, as deduced from the nucleic acid sequence, is present in the induced culture, but not in the uninduced control.
  • Acetohydroxy acid reductoisomerase activity in the cell free extracts is measured using the method described by Arfin and Umbarger (J. Biol. Chem. 244(5):1118-1127 (1969)).
  • the purpose of this prophetic Example is to describe how to clone the HvD gene from E. coli K12 and express it in E. coli BL21 -AI.
  • the HvD gene is amplified from E. coli genomic DNA using PCR.
  • the HvD gene is cloned and expressed in the same manner as the budB gene described in Example 5.
  • Genomic DNA from E. coli is prepared using the Gentra Puregene kit (Gentra Systems, Inc., Minneapolis, MN; catalog number D-5000A).
  • the HvD gene is amplified by PCR using primers N102 and N103 (see Table 2), given as SEQ ID NOs: 15 and 16, respectively, creating a 1.9 kbp product.
  • the forward primer incorporates four bases (CCAC) immediately adjacent to the translational start codon to allow directional cloning into pENTR/SD/D- TOPO (Invitrogen) to generate the plasmid pENTRSDD-TOPOilvD.
  • Clones are submitted for sequencing to confirm that the genes are inserted in the correct orientation and to confirm the sequence.
  • the nucleotide sequence of the open reading frame (ORF) for this gene and the predicted amino acid sequence of the enzyme are given as SEQ ID NO:5 and SEQ ID NO:6, respectively.
  • the HvD gene is transferred to the pDEST 14 (Invitrogen) vector by recombination to generate pDEST14ilvD.
  • the pDEST14ilvD vector is transformed into E. coli BL21 -AI cells and expression from the T7 promoter is induced by addition of arabinose.
  • a protein of the expected molecular weight of about 66 kDa, as deduced from the nucleic acid sequence, is present in the induced culture, but not in the uninduced control.
  • Acetohydroxy acid dehydratase activity in the cell free extracts is measured using the method described by Flint et al. (J. Biol. Chem. 268(20):14732-14742 (1993)).
  • Example 8 Prophetic
  • Branched-Chain Keto Acid Decarboxylase The purpose of this prophetic example is to describe how to clone the kivD gene from Lactococcus lactis and express it in E. coli BL21-AI.
  • a DNA sequence encoding the branched-chain keto acid decarboxylase (kivD) from L. lactis is obtained from GenScript (Piscataway, NJ). The sequence obtained is codon-optimized for expression in both E. coli and B. subtilis and is cloned into pUC57, to form pUC57-kivD.
  • the codon-optimized nucleotide sequence of the open reading frame (ORF) for this gene and the predicted amino acid sequence of the enzyme are given as SEQ ID NO:7 and SEQ ID NO:8, respectively.
  • Ndel and BamHI restriction sites are utilized to clone the 1.7 kbp kivD fragment from pUC57-kivD into vector pET-3a (Novagen, Madison, Wl). This creates the expression clone pET- 3a-kivD.
  • the pET-3a-kivD vector is transformed into E. coli BL21-AI cells and expression from the T7 promoter is induced by addition of arabinose.
  • a protein of the expected molecular weight of about 61 kDa, as deduced from the nucleic acid sequence, is present in the induced culture, but not in the uninduced control.
  • Branched-chain keto acid decarboxylase activity in the cell free extracts is measured using the method described by Smit et al. ⁇ Appl. Microbiol. Biotech nol. 64:396-402 (2003)).
  • the yqhD gene is cloned and expressed in the same manner as the budB gene described in Example 5.
  • Genomic DNA from E. coli is prepared using the Gentra Puregene kit (Gentra Systems, Inc.,
  • the yqhD gene is amplified by PCR using primers N104 and N105 (see Table 2), given as SEQ ID NOs: 17 and 18, respectively, creating a 1.2 kbp product.
  • the forward primer incorporates four bases (CCAC) immediately adjacent to the translational start codon to allow directional cloning into pENTR/SD/D- TOPO (Invitrogen) to generate the plasmid pENTRSDD-TOPOyqhD.
  • Clones are submitted for sequencing to confirm that the genes are inserted in the correct orientation and to confirm the sequence.
  • the nucleotide sequence of the open reading frame (ORF) for this gene and the predicted amino acid sequence of the enzyme are given as SEQ ID NO 9 and SEQ ID NO:10, respectively.
  • the yqhD gene is transferred to the pDEST 14 (Invitrogen) vector by recombination to generate pDEST14yqhD.
  • the pDEST14ilvD vector is transformed into E. coli BL21 - Al cells and expression from the T7 promoter is induced by addition of arabinose.
  • a protein of the expected molecular weight of about 42 kDa, as deduced from the nucleic acid sequence, is present in the induced culture, but not in the uninduced control.
  • Branched-chain alcohol dehydrogenase activity in the cell free extracts is measured using the method described by Sulzenbacher et al. (J. MoI. Biol. 342(2):489-502 (2004)).
  • This prophetic Example is to describe how to construct a transformation vector comprising the genes encoding the five steps in an isobutanol biosynthetic pathway. All genes are placed in a single operon under the control of a single promoter. The individual genes are amplified by PCR with primers that incorporate restriction sites for later cloning and the forward primers contain an optimized E. coli hbosome binding site (AAAGGAGG). PCR products are TOPO cloned into the pCR 4Blunt-TOPO vector and transformed into E. coli Top10 cells (Invitrogen). Plasmid DNA is prepared from the TOPO clones and the sequence of the genes is verified.
  • Restriction enzymes and T4 DNA ligase are used according to manufacturer's recommendations.
  • restriction fragments are gel- purified using QIAquick Gel Extraction kit (Qiagen).
  • the pUC19 vector is modified by Hindlll/Sapl digestion, creating pUC19dHS.
  • the digest removes the lac promoter adjacent to the MCS (multiple cloning site), preventing transcription of the operons in the vector.
  • the budB gene is amplified from K.
  • pneumoniae ATCC 25955 genomic DNA by PCR using primer pair N110 and N111 (see Table 2), given as SEQ ID NOs:19 and 20, respectively, creating a 1.8 kbp product.
  • the forward primer incorporates Sphl and AfIII restriction sites and a hbosome binding site (RBS).
  • the reverse primer incorporates Pad and Nsil restriction sites.
  • the PCR product is cloned into pCR4 Blunt-TOPO creating pCR4 Blunt-TOPO-budB. Plasmid DNA is prepared from the TOPO clones and the sequence of the gene is verified.
  • the HvC gene is amplified from E. coli K12 genomic DNA by PCR using primer pair N112 and N113 (see Table 2) given as SEQ ID NOs:21 and 22, respectively, creating a 1.5 kbp product.
  • the forward primer incorporates Sail and Nhel restriction sites and a RBS.
  • the reverse primer incorporates a Xbal restriction site.
  • the PCR product is cloned into pCR4 Blunt-TOPO creating pCR4 Blunt-TOPO-ilvC. Plasmid DNA is prepared from the TOPO clones and the sequence of the gene is verified.
  • the HvD gene is amplified from E.
  • coli K12 genomic DNA by PCR using primer pair N114 and N115 (see Table 2) given as SEQ ID NOs:23 and 24, respectively, creating a 1.9 kbp product.
  • the forward primer incorporates a Xbal restriction site and a RBS.
  • the reverse primer incorporates a BamHI restriction site.
  • the PCR product is cloned into pCR4 Blunt-TOPO creating pCR4 Blunt-TOPO-ilvD. Plasmid DNA is prepared from the TOPO clones and the sequence of the gene is verified.
  • the kivD gene is amplified from pUC57-kivD (described in Example 8) by PCR using primer pair N116 and N117 (see Table 2), given as SEQ ID NOs:25 and 26, respectively, creating a 1.7 bp product.
  • the forward primer incorporates a BamHI restriction site and a RBS.
  • the reverse primer incorporates a Sacl restriction site.
  • the PCR product is cloned into pCR4 Blunt-TOPO creating pCR4 Blunt-TOPO-kivD. Plasmid DNA is prepared from the TOPO clones and the sequence of the gene is verified.
  • the yqhD gene is amplified from E.
  • coli K12 genomic DNA by PCR using primer pair N118 and N119 (see Table 2) given as SEQ ID NOs:27 and 28, respectively, creating a 1.2 kbp product.
  • the forward primer incorporates a Sacl restriction site.
  • the reverse primer incorporates Spel and EcoRI restriction sites.
  • the PCR product is cloned into pCR4 Blunt- TOPO creating pCR4 Blunt-TOPO-yqhD. Plasmid DNA is prepared from the TOPO clones and the sequence of the gene is verified.
  • the yqhD gene is excised from pCR4 Blunt-TOPO-yqftD with Sacl and EcoRI, releasing a 1.2 kbp fragment. This is ligated with pUC19dHS, which has previously been digested with Sacl and EcoRI. The resulting clone, pUC19dHS- yqhD, is confirmed by restriction digest.
  • the HvC gene is excised from pCR4 Blunt-TOPO-ilvC with Sail and Xbal, releasing a 1.5 kbp fragment. This is ligated with pUC19dHS-yqhD, which has previously been digested with Sail and Xbal.
  • pUC19dHS-ilvC- yqhD is confirmed by restriction digest.
  • the budB gene is then excised from pCR4 BIunt-TOPO-buc/B with Sphl and Nsil, releasing a 1.8 kbp fragment.
  • pUC19dHS-ilvC-yqhD is digested with Sphl and Pstl and ligated with the Sphl/Nsil budB fragment (Nsil and Pstl generate compatible ends), forming pUC19dHS-budB-ilvC-yqhD.
  • a 1.9 kbp fragment containing the HvD gene is excised from pCR4 Blunt-TOPO-ilvD with Xbal and BamHI and ligated with pUC19dHS-budB-ilvC-yqhD, which is digested with these same enzymes, forming pUC19dHS-budB-ilvC-ilvD- yqhD. Finally, kivD is excised from pCR4 Blunt-TOPO-kivD with BamHI and Sacl, releasing a 1.7 kbp fragment.
  • This fragment is ligated with pUC19dHS-budB-ilvC-ilvD-yqhD, which has previously been digested with BamHI and Sacl, forming pUC19dHS-budB-ilvC-ilvD-kivD-yqhD.
  • the pUC19dHS-budB-ilvC-ilvD-kivD-yqhD vector is digested with AfIII and Spel to release a 8.2 kbp operon fragment that is cloned into pBenAS, an E.coli-B. subtilis shuttle vector.
  • Plasmid pBenAS is created by modification of the pBE93 vector, which is described by Nagarajan, (WO 93/24631 , Example 4).
  • NPR Bacillus amyloliquefaciens neutral protease promoter
  • signal sequence signal sequence
  • the phoA gene are removed with a Ncol/Hindlll digest of pBE93.
  • the NPR promoter is PCR amplified from pBE93 by primers BenNF and BenASR, given as SEQ ID NOS:29 and 30, respectively.
  • Primer BenASR incorporates AfIII, Spel, and Hindlll sites downstream of the promoter.
  • the PCR product is digested with Ncol and Hindlll and the fragment is cloned into the corresponding sites in the vector creating pBenAS.
  • the operon fragment is subcloned into the AfIII and Spel sites in pBenAS creating pBen-budB- ilvC-ilvD-kivD-yqhD.
  • EXAMPLE 11 (Prophetic) Expression of the lsobutanol Biosynthetic Pathway in E. coli
  • the purpose of this prophetic Example is to describe how to express an isobutanol biosynthetic pathway in E. coli.
  • the plasmid pBen-budB-ilvC-ilvD-kivD-yqhD constructed as described in Example 10, is transformed into E. coli NM522 (ATCC No. 47000) to give E. coli strain NM522/pBen-budB-ilvC-ilvD-kivD-yqhD and expression of the genes in the operon is monitored by SDS-PAGE analysis, enzyme assay and Western blot analysis. For Western blots, antibodies are raised to synthetic peptides by Sigma-Genosys (The Woodlands, TX).
  • E. coli strain NM522/pBen-budB-ilvC-ilvD-kivD-yqhD is inoculated into a 250 ml_ shake flask containing 50 ml_ of medium and shaken at 250 rpm and 35 0 C.
  • the medium is composed of: glucose (5 g/L), MOPS (0.05 M), ammonium sulfate (0.01 M), potassium phosphate, monobasic (0.005 M), S10 metal mix (1 % (v/v)) yeast extract (0.1 % (w/v)), casamino acids (0.1 % (w/v)), thiamine (0.1 mg/L), proline (0.05 mg/L), and biotin (0.002 mg/L), and is titrated to pH 7.0 with KOH.
  • S10 metal mix contains: MgCI 2 (200 mM), CaCI 2 (70 mM), MnCI 2 (5 mM), FeCI 3 (0.1 mM), ZnCI 2 (0.1 mM), thiamine hydrochloride (0.2 mM), CuSO 4 (172 ⁇ M), CoCI 2 (253 ⁇ M), and Na 2 MoO 4 (242 ⁇ M).
  • isobutanol is detected by HPLC or GC analysis, using methods that are well known in the art, for example, as described in the General Methods section above.
  • EXAMPLE 12 Prophetic Expression of the lsobutanol Biosynthetic Pathway in Bacillus subtilis
  • Example 11 The purpose of this prophetic Example is to describe how to express an isobutanol biosynthetic pathway in Bacillus subtilis. The same approach as described in Example 11 is used.
  • the plasmid pBen-budB-ilvC-ilvD-kivD-yqhD constructed as described in Example 10, is used. This plasmid is transformed into Bacillus subtilis BE1010 (J. Bacteriol. 173:2278-2282 (1991 )) to give B. subtilis strain BE1010/pBen-budB-ilvC-ilvD-kivD-yqhD and expression of the genes in each operon is monitored as described in Example 11.
  • B. subtilis strain BE1010/pBen-budB-ilvC-ilvD-kivD-yqhD is inoculated into a 250 ml_ shake flask containing 50 ml_ of medium and shaken at 250 rpm and 35 0 C for 18 h.
  • the medium is composed of: dextrose (5 g/L), MOPS (0.05 M), glutamic acid (0.02 M), ammonium sulfate (0.01 M), potassium phosphate, monobasic buffer (0.005 M), S10 metal mix (as described in Example 11 , 1 % (v/v)), yeast extract (0.1 % (w/v)), casamino acids (0.1 % (w/v)), tryptophan (50 mg/L), methionine (50 mg/L), and lysine (50 mg/L), and is titrated to pH 7.0 with KOH. After 18 h, isobutanol is detected by HPLC or GC analysis using methods that are well known in the art, for example, as described in the General Methods section above.
  • the budB gene was cloned into the vector pTrc99A.
  • the budB gene was first amplified from pENTRSDD-TOPObudB (described in Example 5) using primers (N110.2 and N111.2, given as SEQ ID NOs:31 and 32, respectively) that introduced Sac ⁇ , Spe ⁇ and Mfe ⁇ sites at the 5' end and BbvC ⁇ , AfIW, and BamH ⁇ sites at the 3' end.
  • the resulting 1.75 kbp PCR product was cloned into pCR4-Blunt TOPO (Invitrogen) and the DNA sequence was confirmed (using N130Seq sequencing primers F1-F4 and R1 -R4, given as SEQ ID NOs:40-47, respectively).
  • the budB gene was then excised from this vector using Sac ⁇ and BamH ⁇ and cloned into pTrc99A (Amann et al. Gene 69(2):301 -315 (1988)), generating pTrc99A::budB.
  • the pTrc99A::budB vector was transformed into E.
  • Acetolactate synthase activity in the cell free extracts was measured as described in Example 5. Three hours after induction with IPTG, an acetolactate synthase activity of 8 units/mg was detected. The control strain carrying only the pTrc99A plasmid exhibited 0.03 units/mg of acetolactate synthase activity.
  • the purpose of this Example was to clone the HvC gene from E. coli K12 and express it in E. coli TOP10.
  • the HvC gene was amplified from E. coli K12 strain FM5 (ATCC 53911 ) genomic DNA using PCR.
  • the HvC gene was cloned and expressed in a similar manner as described for the cloning and expression of HvC in Example 6 above.
  • PCR was used to amplify HvC from the E. coli FM5 genome using primers N112.2 and N113.2 (SEQ ID NOs:33 and 34, respectively).
  • the primers created Sac ⁇ and AfIIW sites and an optimal RBS at the 5' end and Not ⁇ , Nhe ⁇ and BamH ⁇ sites at the 3' end of HvC.
  • the 1.5 kbp PCR product was cloned into pCR4Blunt TOPO according to the manufacturer's protocol (Invitrogen) generating pCR4Blunt TOPO::ilvC.
  • the sequence of the PCR product was confirmed using sequencing primers (N131 SeqF1 -F3, and N131 SeqR1 -R3, given as SEQ ID NOs:48-53, respectively).
  • sequencing primers N131 SeqF1 -F3, and N131 SeqR1 -R3, given as SEQ ID NOs:48-53, respectively.
  • the HvC gene was excised from pCR4Blunt TOPO::ilvC using Sac ⁇ and BamH ⁇ and cloned into pTrc99A.
  • the pTrc99A::ilvC vector was transformed into E. coli TOP10 cells and expression from the Trc promoter was induced by addition of IPTG, as described in Example 13.
  • Cell-free extracts were prepared as described in Example 5.
  • Acetohydroxy acid reductoisomerase activity in the cell free extracts was measured as described in Example 6. Three hours after induction with IPTG, an acetohydroxy acid reductoisomerase activity of 0.026 units/mg was detected. The control strain carrying only the pTrc99A plasmid exhibited less than 0.001 units/mg of acetohydroxy acid reductoisomerase activity.
  • the purpose of this Example was to clone the HvD gene from E. coli K12 and express it in E. coli Top10.
  • the HvD gene was amplified from E. coli K12 strain FM5 (ATCC 53911 ) genomic DNA using PCR.
  • the HvD gene was cloned and expressed in a similar manner as the HvC gene described in Example 14.
  • PCR was used to amplify HvD from the E. coli FM5 genome using primers N114.2 and N115.2 (SEQ ID NOs:35 and 36, respectively).
  • the primers created Sac ⁇ and Nhe ⁇ sites and an optimal RBS at the 5' end and Bsu36 ⁇ , Pac ⁇ and BamH ⁇ sites at the 3' end of HvD.
  • the 1.9 kbp PCR product was cloned into pCR4Blunt TOPO according to the manufacturer's protocol (Invitrogen) generating pCR4Blunt TOPO::ilvD.
  • the sequence of the PCR product was confirmed (sequencing primers N132SeqF1-F4 and N132SeqR1 -R4, given as SEQ ID NOs:54-61 , respectively).
  • the HvD gene was excised from plasmid pCR4Blunt TOPO::ilvD using Sac ⁇ and BamH ⁇ , and cloned into pTrc99A.
  • the pTrc99A::ilvD vector was transformed into E. coli TOP10 cells and expression from the Trc promoter was induced by addition of IPTG, as described in Example 13. Cell-free extracts were prepared as described in Example 5.
  • Acetohydroxy acid dehydratase activity in the cell free extracts was measured as described in Example 7. Three hours after induction with IPTG, an acetohydroxy acid dehydratase activity of 46 units/mg was measured. The control strain carrying only the pTrc99A plasmid exhibited no detectable acetohydroxy acid dehydratase activity.
  • EXAMPLE 16 Cloning and Expression of Branched-Chain Keto Acid Decarboxylase
  • Example 14 The purpose of this Example was to clone the kivD gene from Lactococcus lactis and express it in E. coli TOP10.
  • the kivD gene was cloned and expressed in a similar manner as that described for HvC in Example 14 above.
  • PCR was used to amplify /c/VD from the plasmid pUC57-kivD (see Example 8, above) using primers N116.2 and N117.2 (SEQ ID NOs:37 and 38, respectively).
  • the primers created Sac ⁇ and Pac ⁇ sites and an optimal RBS at the 5' end and Pci ⁇ , AvrW, BgIW and BamH ⁇ sites at the 3' end of kivD.
  • the 1.7 kbp PCR product was cloned into pCR4Blunt TOPO according to the manufacturer's protocol (Invitrogen) generating pCR4Blunt TOPO::kivD.
  • the sequence of the PCR product was confirmed using primers N133SeqF1-F4 and N133SeqR1 -R4 (given as SEQ ID NOs:62-69, respectively).
  • the kivD gene was excised from plasmid pCR4Blunt TOPO::kivD using Sac ⁇ and BamH ⁇ , and cloned into pTrc99A.
  • the pTrc99A::kivD vector was transformed into E. coli TOP10 cells and expression from the Trc promoter was induced by addition of IPTG, as described in Example 13. Cell-free extracts were prepared as described in Example 5.
  • Branched-chain keto acid decarboxylase activity in the cell free extracts was measured as described in Example 8, except that Purpald® reagent (Aldrich, Catalog No. 162892) was used to detect and quantify the aldehyde reaction products. Three hours after induction with IPTG, a branched-chain keto acid decarboxylase activity of greater than 3.7 units/mg was detected. The control strain carrying only the pTrc99A plasmid exhibited no detectable branched-chain keto acid decarboxylase activity.
  • E. coli contains a native gene ⁇ yqhD) that was identified as a 1 ,3- propanediol dehydrogenase (U.S. Patent No. 6,514,733).
  • the YqhD protein has 40% identity to AdhB (encoded by adhB) from Clostridium, a putative NADH-dependent butanol dehydrogenase.
  • AdhB encoded by adhB
  • the yqhD gene was placed under the constitutive expression of a variant of the glucose isomerase promoter 1.6Gl (SEQ ID NO. 70) in E. coli strain MG1655 1.6yqhD::Cm (WO 2004/033646) using ⁇ Red technology (Datsenko and Wanner, Proc. Natl. Acad. Sci.
  • MG1655 1.6yqhD::Cm contains a FRT-CmR-FRT cassette so that the antibiotic marker can be removed.
  • the native promoter was replaced by the 1.5Gl promoter (WO 2003/089621 ) (SEQ ID NO. 71 ), creating strain MG1655 1.5GI-yqhD::Cm, thus, replacing the 1.6Gl promoter of MG1655 1.6yqhD::Cm with the 1.5Gl promoter.
  • Strain MG1655 1.5GI-yqhD::Cm was grown in LB medium to mid- log phase and cell free extracts were prepared as described in Example 5.
  • This strain was found to have NADPH-dependent isobutyraldehyde reductase activity when the cell extracts were assayed by following the decrease in absorbance at 340 nm at pH 7.5 and 35 0 C.
  • a P1 lysate was prepared from MG1655 1.5Gl yqhD::Cm and the cassette was transferred to BL21 (DE3) (Invitrogen) by transduction, creating BL21 (DE3) 1.5GI-yqhD::Cm.
  • the purpose of this Example was to construct a transformation vector comprising the first four genes (i.e., budB, HvC, HvD and kivD) in an isobutanol biosynthetic pathway.
  • the HvC gene was obtained from pTrc99A::ilvC (described in Example 14) by digestion with AfIW and BamH ⁇ and cloned into pTrc99A::budB (described in Example 13), which was digested with AfIW and BamH ⁇ to produce plasmid pTrc99A::budB-ilvC.
  • HvD and kivD genes were obtained from pTrc99A::ilvD (described in Example 15) and pTrc99A::kivD (described in Example 16), respectively, by digestion with Nhe ⁇ and Pac ⁇ (HvD) and Pac ⁇ and BamH ⁇ (kivD). These genes were introduced into pTrc99A::budB- ilvC,which was first digested with Nhe ⁇ and BamH ⁇ , by three-way ligation. The presence of all four genes in the final plasmid, pTrc99A::budB-ilvC- ilvD-kivD, was confirmed by PCR screening and restriction digestion.
  • E. coli isobutanol production strains pTrc99A::budB-ilvC- ilvD-kivD (described in Example 18) was transformed into E. coli MG1655 1.5Gl yqhD::Cm and E. coli B L21 (DE3) 1.5Gl yqhD::Cm (described in Example 17). Transformants were initially grown in LB medium containing 50 ⁇ g/mL kanamycin and 100 ⁇ g/mL carbenicillin.
  • TM3a/glucose medium contained (per liter): glucose (10 g), KH 2 PO 4 (13.6 g), citric acid monohydrate (2.0 g), (NH 4 ) 2 SO 4 (3.0 g),
  • the trace elements solution contained: citric acid H 2 O (4.0 g/L), MnSO4-H 2 O (3.0 g/L), NaCI (1.0 g/L), FeSO4-7H 2 O (0.10 g/L), CoCI 2 -6H 2 O (0.10 g/L), ZnSO4-7H 2 O (0.10 g/L), CuSO4-5H 2 O (0.010 g/L), H3BO3 (0.010 g/L), and Na 2 Mo ⁇ 4- 2H 2 O (0.010 g/L).
  • the flasks were inoculated at a starting OD 6 oo of ⁇ 0.01 units and incubated at 34 0 C with shaking at 300 rpm.
  • the flasks containing 50 mL of medium were closed with 0.2 ⁇ m filter caps; the flasks containing 150 mL of medium were closed with sealed caps.
  • IPTG was added to a final concentration of 0.04 mM when the cells reached an OD 6 oo of > 0.4 units.
  • HPLC Showa Denko America, Inc.
  • sucrose utilization gene cluster cscBKA was isolated from genomic DNA of a sucrose-utilizing E. coli strain derived from ATCC strain 13281.
  • the sucrose utilization genes (cscA, cscK, and cscB) encode a sucrose hydrolase (CscA), given as SEQ ID NO:139, D-fructokinase (CscK), given as SEQ ID NO:140, and sucrose permease (CscB), given as SEQ ID NO:141.
  • the sucrose-specific repressor gene cscR was not included so that the three genes cscBKA were expressed constitutively from their native promoters in E. coli.
  • Genomic DNA from the sucrose-utilizing E. coli strain was digested to completion with BamH ⁇ and EcoR ⁇ . Fragments having an average size of about 4 kbp were isolated from an agarose gel and were ligated to plasmid pLitmus28 (New England Biolabs), digested with BamH ⁇ and EcoR ⁇ and transformed into ultracompetent E. co// TOP10F' cells (Invitrogen). The transformants were streaked onto MacConkey agar plates containing 1 % sucrose and ampicillin (100 ⁇ g/mL) and screened for the appearance of purple colonies.
  • Plasmid DNA was isolated from the purple transformants, and sequenced with M13 Forward and Reverse primers (Invitrogen), and Scr1 -4 (given as SEQ ID NOs:72-75, respectively).
  • the plasmid containing cscB, cscK, and cscA (cscBKA) genes was designated pScr1.
  • pScr1 To create a sucrose utilization plasmid that was compatible with the isobutanol pathway plasmid (Example 18), the operon from pScri was subcloned into pBHR1 (MoBiTec, Goettingen, Germany).
  • the cscBKA genes were isolated by digestion of pScri with Xho ⁇ (followed by incubation with Klenow enzyme to generate blunt ends) and then by digestion with Age ⁇ . The resulting 4.2 kbp fragment was ligated into pBHR1 that had been digested with ⁇ /ael and Age ⁇ , resulting in the 9.3 kbp plasmid pBHR1 ::cscBKA.
  • sucrose plasmid pBHR1 ::cscBKA was transformed into E. coli BL21 (DE3) 1.5 yqhD /pTrc99A::budB-ilvC-ilvD-kivD and E. coli MG1655 1.5yqhD /pTrc99A::budB-ilvC-ilvD-kivD (described in Example 19) by electroporation. Transformants were first selected on LB medium containing 100 ⁇ g/mL ampicillin and 50 ⁇ g/mL kanamycin and then screened on MacConkey sucrose (1 %) plates to confirm functional expression of the sucrose operon.
  • isobutanol For production of isobutanol, strains were grown in TM3a minimal defined medium (described in Example 19) containing 1 % sucrose instead of glucose, and the culture medium was analyzed for the amount of isobutanol produced, as described in Example 19, except that samples were taken 14 h after induction. Again, no isobutanol was detected in control strains carrying only the pTrc99A vector (results not shown). Molar selectivities and titers of isobutanol produced by MG1655 1.5yqhD carrying pTrc99A::budB-ilvC-ilvD-kivD are shown in Table 14. Similar results were obtained with the analogous BL21 (DE3) strain.
  • the GPD promoter (SEQ ID NO:76) and CYC1 terminator (SEQ ID NO:77) were fused to the alsS gene from Bacillus subtilis (SEQ ID NO:78), the FBA promoter (SEQ ID NO:79) and CYC1 terminator were fused to the ILV5 gene from S. cerevisiae (SEQ ID NO:80), the ADH1 promoter (SEQ ID NO:81 ) and ADH 1 terminator (SEQ ID NO:82) were fused to the ILV3 gene from S.
  • the primers given in Table 15, were designed to include restriction sites for cloning promoter/gene/terminator products into E. co//-yeast shuttle vectors from the pRS400 series (Christianson et al. Gene 110:119-122 (1992)) and for exchanging promoters between constructs. Primers for the 5' ends of ILV5 and ILV3 (N138 and N155, respectively, given as SEQ ID NOs: 95 and 107, respectively) generated new start codons to eliminate mitochondrial targeting of these enzymes.
  • the plasmids were transformed into either Saccharomyces cerevisiae BY4743 (ATCC 201390) or YJR148w (ATCC 4036939) to assess enzyme specific activities using the enzyme assays described in Examples 5-8 and Examples 13-16. For the determination of enzyme activities, cultures were grown to an OD600 of
  • Plasmids pRS423::CUP1 -alsS+FBA-ILV3 and pHR81 ::FBA- ILV5+GPM-kivD (described in Example 21 ) were transformed into Saccharomyces cerevisiae YJR148w to produce strain YJR148w/pRS423::CUP1 -alsS+FBA-ILV3/ pHR81 ::FBA-ILV5+ GPM-kivD.
  • a control strain was prepared by transforming vectors pRS423 and pHR81 (described in Example 21 ) into Saccharomyces cerevisiae YJR148w (strain YJR148w/pRS423/pHR81 ).
  • Aerobic cultures were grown in 175 ml_ capacity flasks containing 50 ml_ of medium in an Innova4000 incubator (New Brunswick Scientific, Edison, NJ) at 30 0 C and 200 rpm.
  • Low oxygen cultures were prepared by adding 45 ml_ of medium to 60 ml_ serum vials that were sealed with crimped caps after inoculation and kept at 30 0 C.
  • Sterile syringes were used for sampling and addition of inducer, as needed. Approximately 24 h after inoculation, the inducer CuSO 4 was added to a final concentration of 0.03 mM. Control cultures for each strain without CuSO 4 addition were also prepared.
  • strain suffixes "a”, “b”, and “c” indicate separate isolates. The results indicate that, when grown on glucose or sucrose under both aerobic and low oxygen conditions, strain YJR148w/pRS423::CUP1 - alsS+FBA-ILV3/ pHR81 ::FBA-ILV5+ GPM-kivD produced consistently higher levels of isobutanol than the control strain.
  • Plasmids pRS425::CUP1 -alsS+FBA-ILV3 and pRS426::GAL1- ILV5+GPM-kivD were transformed into Saccharomyces cerevisiae YJR148w to produce strain
  • a control strain was prepared by transforming vectors pRS425 and pRS426 (described in Example 21 ) into Saccharomyces cerevisiae YJR148w (strain YJR148w/pRS425/pRS426). Strains were maintained on synthetic complete medium, as described in Example 22.
  • the purpose of this Example was to express an isobutanol biosynthetic pathway in Bacillus subtilis.
  • the five genes of the isobutanol pathway (pathway steps (a) through (e) in Figure 1 ) were split into two operons for expression.
  • HvC and bdhB encoding acetohydroxy acid isomeroreductase and butanol dehydrogenase, respectively, were cloned into an expression vector and transformed into the Bacillus strain carrying the integrated isobutanol genes.
  • Bacillus integration vectors pFP988DssPspac and pFP988DssPgroE were used for the chromosomal integration of the three genes, budB (SEQ ID NO:1 ), HvD (SEQ ID NO:5), and kivD (SEQ ID NO:7).
  • Both plasmids contain an E. coli replicon from pBR322, an ampicillin antibiotic marker for selection in E. coli and two sections of homology to the sacB gene in the Bacillus chromosome that direct integration of the vector and intervening sequence by homologous recombination.
  • spac promoter PgroE
  • groEL groEL promoter
  • the promoter region also contains the lacO sequence for regulation of expression by a lacl repressor protein.
  • the sequences of pFP988DssPspac (6,341 bp) and pFP988DssPgroE (6,221 bp) are given as SEQ ID NO:142 and SEQ ID NO:143 respectively.
  • the cassette with three genes budB-ilvD-kivD was constructed by deleting the HvC gene from plasmid pTrc99a budB-ilvC-ilvD-kivD.
  • the construction of the plasmid pTrc99A::budB-ilvC-ilvD-kivD is described in Example 18.
  • Plasmid pTrc99A::budB-ilvC-ilvD-kivD was digested with AfIII and Nhel, treated with the Klenow fragment of DNA polymerase to make blunt ends, and the resulting 9.4 kbp fragment containing pTrc99a vector, budB, HvD, and kivD was gel-purified.
  • the 9.4 kbp vector fragment was self-ligated to create pTrc99A::budB-ilvD-kivD, and transformed into DH5 ⁇ competent cells (Invitrogen).
  • a clone of pTrc99a budB-ilvD-kivD was confirmed for the HvC gene deletion by restriction mapping.
  • the resulting plasmid pTrc99A::budB-ilvD-kivD was digested with Sacl and treated with the Klenow fragment of DNA polymerase to make blunt ends. The plasmid was then digested with BamHI and the resulting 5,297 bp budB-ilvD-kivD fragment was gel-purified.
  • the 5,297 bp budB-ilvD-kivD fragment was ligated into the Smal and BamHI sites of the integration vector pFP988DssPspac.
  • the ligation mixture was transformed into DH5 ⁇ competent cells. Transformants were screened by PCR amplification of the 5.3 kbp budB-ilvD-kivD fragment with primers T-budB(BamHI) (SEQ ID NO:144) and B-kivD(BamHI) (SEQ ID NO:145).
  • the correct clone was named pFP988DssPspac-budB-ilvD-kivD.
  • Plasmid pFP988DssPspac-budB-ilvD-kivD was prepared from the E. coli transformant, and transformed into B. subtilis BE1010 competent cells, which had been prepared as described by Doyle et al. (J. Bacteriol. 144:957 (1980)). Competent cells were harvested by centrifugation and the cell pellets were resuspended in a small volume of the supernatant. To one volume of competent cells, two volumes of SPII-EGTA medium (Methods for General and Molecular Bacteriology, P. Gerhardt et al., Ed., American Society for Microbiology, Washington, DC (1994)) was added.
  • ⁇ sacB::Pspac-budB-ilvD-kivD #2-3-2 and B. subtilis BE1010 ⁇ sacB::Pspac-budB-ilvD-kivD #6-12-7 indicated that the activities of BudB, HvD and KivD were low under the control of the spac promoter (Pspac).
  • the Pspac promoter was replaced by a PgroE promoter from plasmid pHT01 (MoBitec, Goettingen, Germany).
  • the PgroE promoter was PCR- amplified from plasmid pHT01 with primers T-groE(Xhol) (SEQ ID NO:146).
  • Plasmid pFP988DssPspac-budB-ilvD-kivD was digested with Spel and Pmel and the resulting 5,313 bp budB-ilvD-kivD fragment was gel- purified.
  • the budB-ilvD-kivD fragment was ligated into Spel and Pmel sites of pFP988DssPgroE and transformed into DH5 ⁇ competent cells.
  • Positive clones were screened for a 1 ,690 bp PCR product by PCR amplification with primers T-groEL (SEQ ID NO:149) and N111 (SEQ ID NO:20). The positive clone was named pFP988DssPgroE-budB-ilvD-kivD.
  • Plasmid pFP988DssPgroE-budB-ilvD-kivD was prepared from the E. coli transformant, and transformed into Bacillus subtilis BE1010 competent cells as described above. Transformants were screened by PCR amplification with primers N130SeqF1 (SEQ ID NO:40) and
  • N130SeqR1 SEQ ID NO:44
  • N133SeqF1 SEQ ID NO:62
  • N133SeqR1 SEQ ID NO:66
  • Positive integrants showed the expected 1.7 kbp budB and 1.7 kbp kivD PCR products.
  • Two positive integrants were isolated and named B. subtilis BE1010 ⁇ sacB::PgroE- budB-ilvD-kivD #1 -7 and B. subtilis BE101010 ⁇ sacB::PgroE-budB-ilvD-kivD #8-16.
  • Plasmid Expression of HvC and bdhB genes Two remaining isobutanol genes, HvC and bdhB, were expressed from a plasmid. Plasmid pHT01 (MoBitec), a Bacillus-E. coli shuttle vector, was used to fuse an HvC gene from B. subtilis to a PgroE promoter so that the HvC gene was expressed from the PgroE promoter containing a lacO sequence. The HvC gene, given as SEQ ID NO:186, was PCR-amplified from B.
  • subtilis BR151 ATCC 33677 genomic DNA with primers T-ilvCB.s.(BamHI) (SEQ ID NO:150) and B-ilvCB.s.(Spel BamHI) (SEQ ID NO:151 ).
  • the 1 ,067 bp HvC PCR product was digested with BamHI and ligated into the BamHI site of pHT01.
  • the ligation mixture was transformed into DH5 ⁇ competent cells. Positive clones were screened for a 1 ,188 bp PCR product by PCR amplification with primers T-groEL and B-NvB. s. (Spel BamHI).
  • the positive clone was named pHT01 -HvC(B. s). Plasmid pHT01 -HvC(B. s) was used as a template for PCR amplification of the PgroE-ilvC fused fragment.
  • Plasmid pBD64 (Minton et al., Nucleic Acids Res. 18:1651 (1990)) is a fairly stable vector for expression of foreign genes in B. subtilis and contains a repB gene and chloramphenicol and kanamycin resistance genes for selection in B. subtilis. This plasmid was used for expression of HvC and bdhB under the control of a PgroE promoter. To clone PgroE-ilvC, bdhB and a lacl repressor gene into plasmid pBD64, a one-step assembly method was used (Tsuge et al., Nucleic Acids Res. 31 :e133 (2003)).
  • a 3,588 bp pBD64 fragment containing a repB gene, which included the replication function, and the kanamycin antibiotic marker was PCR- amplified from pBD64 with primers T-BD64(Dralll) (SEQ ID NO:152), which introduced a Dralll sequence (CACCGAGTG), and B-BD64(Dralll) (SEQ ID NO:153), which introduced a Dralll sequence (CACCTGGTG).
  • a 1 ,327 bp lacl repressor gene was PCR-amplified from pMUTIN4 (Vagner et al., Microbiol.
  • a 1.2 kbp bdhB gene (SEQ ID NO:158) was PCR- amplified from Clostridium acetobutylicum (ATCC 824) genomic DNA with primers T-bdhB(Dralll) (SEQ ID NO:159), which introduced a Dralll sequence (CACACGGTG), and B-bdhB(rrnBT1 Dralll) (SEQ ID NO:160), which introduced a Dralll sequence (CACTCGGTG).
  • the three underlined letters in the variable region of the Dralll recognition sequences were designed for specific base-pairing to assemble the four fragments with an order of pBD64-/ac/-PgroE/Vi/C- ⁇ bc//7 ⁇ .
  • Dralll fragments 3,588 bp pBD64, lacl, PgroE/Vi/C, and bdhB were gel-purified using a QIAGEN gel extraction kit (QIAGEN).
  • QIAGEN QIAGEN gel extraction kit
  • the ligation solution was then incubated at 16 0 C overnight.
  • the ligation generated high molecular weight tandem repeat DNA.
  • the ligated long, linear DNA mixture was directly transformed into competent B. subtilis BE1010, prepared as described above.
  • subtilis preferentially takes up long repeated linear DNA forms, rather than circular DNA to establish a plasmid.
  • the culture was spread onto an LB plate containing 10 ⁇ g/mL of kanamycin for selection.
  • Positive recombinant plasmids were screened by Dralll digestion, giving four fragments with an expected size of 3,588 bp (pBD64), 1 ,327 bp ⁇ lad), 1 ,224 bp (PgorE-//i/C), and 1 ,194 bp (bdhB).
  • the positive plasmid was named pBDPgroE-ilvC(B.s.)-bdhB.
  • subtilis BE1010 ⁇ sacB::PgroE-budB-ilvD-kivD #8-16 were prepared as described above, and transformed with plasmid pBDPgroE-ilvC(B.s.)- bdhB, yielding B. subtilis BE1010 ⁇ sacB::PgroE-budB-ilvD-kivD #1-
  • the two recombinant strains were inoculated in either 25 ml_ or 100 ml_ of glucose medium containing kanamycin (10 ⁇ g /ml_) in 125 ml_ flasks to simulate high and low oxygen conditions, respectively, and aerobically grown at 37 0 C with shaking at 200 rpm.
  • the medium consisted of 10 mM (NhU) 2 SO 4 , 5 mM potassium phosphate buffer (pH 7.0), 100 mM MOPS/KOH buffer (pH 7.0), 20 mM glutamic acid/KOH (pH 7.0), 2% S10 metal mix, 1 % glucose, 0.01 % yeast extract, 0.01 % casamino acids, and 50 ⁇ g/mL each of L-tryptophan, L-methionine, and L-lysine.
  • the S10 metal mix consisted of 200 mM MgCI 2 , 70 mM CaCI 2 , 5 mM MnCI 2 , 0.1 mM FeCI 3 , 0.1 mM ZnCI 2 , 0.2 mM thiamine hydrochloride, 0.172 mM CuSO 4 , 0.253 mM CoCI 2 , and 0.242 mM Na 2 MoO 4 .
  • the cells were induced with 1.0 mM isopropyl- ⁇ -D-thiogalactopyranoiside (IPTG) at early-log phase (OD600 of approximately 0.2).
  • B. subtilis a is B. subtilis BE1010 ⁇ sacB::PgroE-budB-ilvD-kivD #1-7/ pBDPgroE-ilvC(B.s.)-bdhB
  • subtilis b is B. subtilis BE1010 ⁇ sacB::PgroE-budB-ilvD-kivD #8-16/ pBDPgroE-ilvC(B.s.)-bdhB
  • sucrose medium containing kanamycin (10 ⁇ g /mL) in 125 mL flasks to simulate high and medium oxygen levels, and grown at 37 0 C with shaking at 200 rpm.
  • the sucrose medium was identical to the glucose medium except that glucose (10 g/L) was replaced with 10 g/L of sucrose.
  • the cells were uninduced, or induced with 1.0 mM isopropyl- ⁇ -D-thiogalactopyranoiside (IPTG) at early-log phase (OD600 of approximately 0.2).
  • IPTG isopropyl- ⁇ -D-thiogalactopyranoiside
  • OD600 OD600 of approximately 0.2
  • HPLC refractive index
  • B. subtilis a is B. subtilis BE1010 ⁇ sacB::PgroE-budB-ilvD-kivD #1-7/ pBDPgroE-ilvC(B.s.)-bdhB
  • the purpose of this prophetic Example is to describe how to express an isobutanol biosynthetic pathway in Lactobacillus plantarum.
  • the five genes of the isobutanol pathway, encoding five enzyme activities, are divided into two operons for expression.
  • the budB, HvD and kivD genes, encoding the enzymes acetolactate synthase, acetohydroxy acid dehydratase, and branched-chain ⁇ -keto acid decarboxylase, respectively, are integrated into the chromosome of Lactobacillus plantarum by homologous recombination using the method described by Hols et al. ⁇ Appl. Environ. Microbiol. 60:1401-1413 (1994)).
  • HvC and bdhB encoding the enzymes acetohydroxy acid reductoisomerase and butanol dehydrogenase, respectively
  • HvC and bdhB encoding the enzymes acetohydroxy acid reductoisomerase and butanol dehydrogenase, respectively
  • the budB-ilvD-kivD cassette under the control of the synthetic P11 promoter (Rud et al., Microbiology 152:1011 -1019 (2006)) is integrated into the chromosome of Lactobacillus plantarum ATCC BAA- 793 (NCIMB 8826) at the IdhLI locus by homologous recombination.
  • NCIMB 8826 Lactobacillus plantarum ATCC BAA- 793
  • the 1986 bp PCR fragment is cloned into pCR4Blunt-TOPO and sequenced.
  • the pCR4Blunt-TOPO-ldhL1 clone is digested with EcoRV and Aatll releasing a 1982 bp IdhLI fragment that is gel-purified.
  • the integration vector pFP988, given as SEQ ID NO:177 is digested with Hindlll and treated with Klenow DNA polymerase to blunt the ends.
  • the linearized plasmid is then digested with Aatll and the 2931 bp vector fragment is gel purified.
  • the EcoRV/Aatll IdhLI fragment is ligated with the pFP988 vector fragment and transformed into E. coli Top10 cells. Transformants are selected on LB agar plates containing ampicillin (100 ⁇ g/mL) and are screened by colony PCR to confirm construction of pFP988-ldhL.
  • the Cm gene with its promoter is PCR amplified from pC194 (GenBank NC_002013, SEQ ID NO:267) with primers Cm F (SEQ ID NO:163) and Cm R (SEQ ID NO:164), amplifying a 836 bp PCR product.
  • This PCR product is cloned into pCR4Blunt-TOPO and transformed into E. coli Top10 cells, creating pCR4Blunt-TOPO-Cm.
  • the Cm cassette is digested from pCR4Blunt-TOPO- Cm as an 828 bp Mlul/Swal fragment and is gel purified.
  • the IdhL- homology containing integration vector pFP988-ldhL is digested with MIuI and Swal and the 4740 bp vector fragment is gel purified.
  • the Cm cassette fragment is ligated with the pFP988-ldhL vector creating pFP988- DldhL::Cm.
  • budB-ilvD-kivD cassette from pFP988DssPspac-budB- ilvD-kivD, described in Example 24, is modified to replace the amylase promoter with the synthetic P11 promoter. Then, the whole operon is moved into pFP988-DldhL::Cm.
  • the P11 promoter is built by oligonucleotide annealing with primer P11 F-Stul (SEQ ID NO:165) and P11 R-Spel (SEQ ID NO:166). The annealed oligonucleotide is gel- purified on a 6% Ultra PAGE gel (Embi Tec, San Diego, CA).
  • the plasmid pFP988DssPspac-budB-ilvD-kivD containing the amylase promoter, is digested with Stul and Spel and the resulting 10.9 kbp vector fragment is gel-purified.
  • the isolated P11 fragment is ligated with the digested pFP988DssPspac-budB-ilvD-kivD to create pFP988-P11 -budB-ilvD-kivD.
  • Plasmid pFP988-P11 -budB-ilvD-kivD is then digested with Stul and BamHI and the resulting 5.4 kbp P11 -budB-ilvD-kivD fragment is gel- purified.
  • pFP988-DldhL::Cm is digested with Hpal and BamHI and the 5.5 kbp vector fragment isolated.
  • the budB-ilvD-kivD operon is ligated with the integration vector pFP988-Dldhl_::Cm to create pFP988-Dldhl_-P11 - budB-ilvD-kivD::Cm.
  • Electrocompetent cells of L. plantarum are prepared as described by Aukrust, T.W., et al. (In: Electroporation Protocols for Microorganisms; Nickoloff, J. A., Ed.; Methods in Molecular Biology, Vol. 47; Humana Press, Inc., Totowa, NJ, 1995, pp 201 -208).
  • MRSSM medium MRS medium supplemented with 0.5 M sucrose and 0.1 M MgCl2
  • Electroporated cells are plated for selection on MRS plates containing chloramphenicol (10 ⁇ g/mL) and incubated at 37 0 C.
  • Transformants are initially screened by colony PCR amplification to confirm integration, and initial positive clones are then more rigorously screened by PCR amplification with a battery of primers.
  • Plasmid Expression of HvC and bdhB genes The remaining two isobutanol genes are expressed from plasmid pTRKH3 (O'Sullivan DJ and Klaenhammer TR, Gene 137:227-231 (1993)) under the control of the L plantarum IdhL promoter (Ferain et al., J. Bacteriol. 176:596-601 (1994)).
  • the IdhL promoter is PCR amplified from the genome of L. plantarum ATCC BAA-793 using primers PldhL F-Hindlll (SEQ ID NO:167) and PldhL R-BamHI (SEQ ID NO:168).
  • the 411 bp PCR product is cloned into pCR4Blunt-TOPO and sequenced.
  • the resulting plasmid, pCR4Blunt- TOPO-PIdhL is digested with Hindlll and BamHI releasing the PldhL fragment.
  • Plasmid pTRKH3 is digested with Hindlll and Sphl and the gel- purified vector fragment is ligated with the PldhL fragment and the gel- purified 2.4 kbp BamHI/Sphl fragment containing ilvC(B.s.)-bdhB from the Bacillus expression plasmid pBDPgroE-ilvC(B.s.)-bdhB (Example 24) in a three-way ligation.
  • the ligation mixture is transformed into E. coli Top 10 cells and transformants are grown on Brain Heart Infusion (BHI, Difco Laboratories, Detroit, Ml) plates containing erythromycin (150 mg/L).
  • Transformants are screened by PCR to confirm construction.
  • the resulting expression plasmid, pTRKH3-ilvC(B.s.)-bdhB is transformed into L. plantarum ⁇ ldhLI ::budB-ilvD-kivD::Cm by electroporation, as described above.
  • L. plantarum ⁇ ldhLI ::budB-ilvD-kivD::Cm containing pTRKH3- ilvC(B.s.)-bdhB is inoculated into a 250 mL shake flask containing 50 mL of MRS medium plus erythromycin (10 ⁇ g/mL) and grown at 37 0 C for 18 to 24 h without shaking, after which isobutanol is detected by HPLC or GC analysis, as described in the General Methods section.
  • Plasmid pTRKH3 (O'Sullivan DJ and Klaenhammer TR, Gene 137:227-231 (1993)), is used for expression of the five genes (budB, HvC, HvD, kivD, bdhB) of the isobutanol pathway in one operon.
  • pTRKH3 contains an E. coli plasmid p15A replication origin, the pAM ⁇ i replicon, and two antibiotic resistance selection markers for tetracycline and erythromycin. Tetracycline resistance is only expressed in E. coli, and erythromycin resistance is expressed in both E. coli and Gram-positive bacteria. Plasmid pAM ⁇ i derivatives can replicate in E.
  • faecalis (Poyart et al., FEMS Microbiol. Lett. 156:193-198 (1997)).
  • the inducible nisA promoter (PnisA) which has been used for efficient control of gene expression by nisin in a variety of Gram-positive bacteria including Enterococcus faecalis (Eichenbaum et al., Appl. Environ. Microbiol. 64:2763-2769 (1998)), is used to control expression of the five desired genes encoding the enzymes of the isobutanol biosynthetic pathway.
  • the plasmid pTrc99A::budB-ilvC-ilvD-kivD (described in Example 18), which contains the isobutanol pathway operon, is modified to replace the E. coli HvC gene (SEQ ID NO:3) with the B. subtilis HvC gene (SEQ ID NO:184). Additionally, the bdhB gene(SEQ ID NO:158) from Clostridium acetobutylicum is added to the end of the operon.
  • the bdhB gene from pBDPgroE-ilvC(B.s.)-bdhB (described in Example 24) is amplified using primers F-bdhB-Avrll (SEQ ID NO:169) and R-bdhB-BamHI (SEQ ID NO:170), and then TOPO cloned and sequenced.
  • the 1194 bp bdhB fragment is isolated by digestion with Avrll and BamHI, followed by gel purification.
  • This bdhB fragment is ligated with pTrc99A::budB-ilvC-ilvD- kivD that has previously been digested with Avrll and BamHI and the resulting fragment is gel purified.
  • the ligation mixture is transformed into E. coli Top10 cells by electroporation and transformants are selected following overnight growth at 37 0 C on LB agar plates containing ampicillin (100 ⁇ g/mL). The transformants are then screened by colony PCR to confirm the correct clone containing pTrc99A::budB-ilvC-ilvD-kivD-bdhB. Next, /VvC(B.s.) is amplified from pBDPgroE-ilvC(B.s.)-bdhB
  • the ligation mixture is transformed into E. coli Top10 cells by electroporation and transformants are selected following overnight growth at 37 0 C on LB agar plates containing ampicillin (100 ⁇ g/mL). The transformants are then screened by colony PCR to confirm the correct clone containing pTrc99A::budB-ilvC(B.s.)-ilvD-kivD- bdhB.
  • the nisA promoter Choandrapati et al., MoI. Microbiol.
  • Transformants are selected following overnight growth at 37 0 C on LB agar plates containing erythromycin (25 ⁇ g/mL). The transformants are then screened by colony PCR to confirm the correct clone of pTRKH3-PnisA.
  • Plasmid pTRKH3-PnisA is digested with Spel and BamHI, and the vector is gel-purified.
  • Plasmid pTrc99A::budB-ilvC(B.s)-ilvD-kivD-bdhB, described above, is digested with Spel and BamHI, and the 7.5 kbp fragment is gel-purified.
  • the 7.5 kbp budB-ilvC(B.s)-ilvD-kivD-bdhB fragment is ligated into the pTRKH3-PnisA vector at the Spel and BamHI sites. The ligation mixture is transformed into E.
  • coli Top10 cells by electroporation and transformants are selected following overnight growth on LB agar plates containing erythromycin (25 ⁇ g/mL) at 37 0 C. The transformants are then screened by colony PCR. The resulting plasmid is named pTRKH3-PnisA-budB-ilvC(B.s)-ilvD-kivD-bdhB. This plasmid is prepared from the E. coli transformants and transformed into electro- competent E. faecalis V583 cells by electroporation using methods known in the art (Aukrust, T.W., et al. In: Electroporation Protocols for
  • the plasmid containing pSH71 origin of replication is compatible with pAM ⁇ i derivatives in E. faecalis (Eichenbaum et al., supra). Double drug resistant transformants are selected on LB agar plates containing erythromycin (25 ⁇ g/mL) and spectinomycin (100 ⁇ g/mL), grown at 37 0 C.
  • an expression plasmid pTRKH3-PnisA-budB-ilvC(B.s)-ilvD-kivD-bdhB
  • pSH71 -nisRK a regulatory plasmid
  • EXAMPLE 27 Increased tolerance of Saccharomvces cerevisiae to isobutanol at decreased growth temperatures
  • Tolerance levels were determined for yeast strain Saccharomyces cerevisiae BY4741 (ATCC 201388) at 25 0 C and 30 0 C as follows.
  • the strain was cultured in YPD medium. Overnight cultures in the absence of any test compound were started in 25 mL of YPD medium in 150 mL flasks with incubation at 30 0 C or at 25 0 C in shaking water baths. The next morning, each overnight culture was diluted into a 500 mL flask containing 300 mL of fresh medium to an initial OD600 of about 0.1. The flasks were incubated in shaking water baths at 30 0 C or 25 °, using the same temperature as used for each overnight culture.
  • the large cultures were incubated for 3 hours and then were split into flasks in the absence (control) and in the presence of 2% or 3% of isobutanol. Growth was followed by measuring OD600 for six hours after addition of the isobutanol. The ⁇ OD 6 oo was calculated by subtracting the initial OD 6 oo from the final OD 6 Oo at 6 hours.

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Abstract

A method for the production of isobutanol by fermentation using a microbial production host is disclosed. The method employs a reduction in temperature during the fermentation process that results in a more robust tolerance of the production host to the butanol product.

Description

TITLE METHOD FOR THE PRODUCTION OF ISOBUTANOL
FIELD OF THE INVENTION The invention relates to a method for the production of isobutanol by fermentation using a recombinant microbial host. Specifically, the method employs a decrease in temperature during fermentation that results in more robust tolerance of the production host to the isobutanol product. BACKGROUND OF THE INVENTION
Butanol is an important industrial chemical, useful as a fuel additive, as a feedstock chemical in the plastics industry, and as a foodgrade extractant in the food and flavor industry. Each year 10 to12 billion pounds of butanol are produced by petrochemical means and the need for this commodity chemical will likely increase.
Methods for the chemical synthesis of isobutanol are known, such as oxo synthesis, catalytic hydrogenation of carbon monoxide (Ullmann's Encyclopedia of Industrial Chemistry, 6th edition, 2003, Wiley-VCHVerlag GmbH and Co., Weinheim, Germany, Vol. 5, pp. 716-719) and Guerbet condensation of methanol with n-propanol (Carlini et al., J. MoI. Catal. A:Chem. 220:215-220 (2004)). These processes use starting materials derived from petrochemicals and are generally expensive and are not environmentally friendly. The production of isobutanol from plant-derived raw materials would minimize greenhouse gas emissions and would represent an advance in the art.
Isobutanol is produced biologically as a by-product of yeast fermentation. It is a component of "fusel oil" that forms as a result of incomplete metabolism of amino acids by this group of fungi. Isobutanol is specifically produced from catabolism of L-valine. After the amine group of L-valine is harvested as a nitrogen source, the resulting α-keto acid is decarboxylated and reduced to isobutanol by enzymes of the so-called Ehrlich pathway (Dickinson et al., J. Biol. Chem. 273(40):25752-25756 (1998)). Yields of fusel oil and/or its components achieved during beverage fermentation are typically low. For example, the concentration of isobutanol produced in beer fermentation is reported to be less than 16 parts per million (Garcia et al., Process Biochemistry 29:303-309 (1994)). Addition of exogenous L-valine to the fermentation increases the yield of isobutanol, as described by Dickinson et al., supra, wherein it is reported that a yield of isobutanol of 3 g/L is obtained by providing L-valine at a concentration of 20 g/L in the fermentation. However, the use of valine as a feed-stock would be cost prohibitive for industrial scale isobutanol production. The biosynthesis of isobutanol directly from sugars would be economically viable and would represent an advance in the art.
Recombinant microbial production hosts expressing an isobutanol biosynthetic pathway have been described (Donaldson et al., copending and commonly owned U.S. Patent Application Publication No. US20070092957 A1 ). However, biological production of isobutanol is believed to be limited by butanol toxicity to the host microorganism used in the fermentation.
Some microbial strains that are tolerant to isobutanol are known in the art (Bramucci et al., copending and commonly owned U.S. Patent Application Nos. 11/743220and 11/761497). However, biological methods of producing isobutanol to higher levels are required for cost effective commercial production.
There have been reports describing the effect of temperature on the tolerance of some microbial strains to ethanol. For example, Amartey et al. (Biotechnol. Lett. 13(9):627-632 (1991 )) disclose that Bacillus stearothermophillus is less tolerant to ethanol at 70 0C than at 60 0C.
Herrero et al. {Appl. Environ. Microbiol. 40(3):571 -577 (1980)) report that the optimum growth temperature of a wild-type strain of Clostridium thermocellum decreases as the concentration of ethanol challenge increases, whereas the optimum growth temperature of an ethanol- tolerant mutant remains constant. Brown et al. (Biotechnol. Lett. 4(4):269- 274 (1982)) disclose that the yeast Saccharomyces uvarum is more resistant to growth inhibition by ethanol at temperatures 5 0C and 10 0C below its growth optimum of 35 0C. However, fermentation became more resistant to ethanol inhibition with increasing temperature. Additionally, Van Uden (CRC Cήt Rev. Biotechnol. 1 (3):263-273 (1984)) report that ethanol and other alkanols depress the maximum and the optimum growth temperature for growth of Saccharomyces cerevisiae while thermal death is enhanced. Moreover, Lewis et al. (U.S. Patent Application Publication No. 2004/0234649) describe methods for producing high levels of ethanol during fermentation of plant material comprising decreasing the temperature during saccharifying, fermenting, or simultaneously saccharifying and fermenting.
Much less is known about the effect of temperature on the tolerance of microbial strains to butanols. Harada (Hakko Kyokaishi 20:155-156 (1962)) discloses that the yield of 1 -butanol in acetone- butanol-ethanol (ABE) fermentation is increased from 18.4%-18.7% to 19.1 %-21.2% by lowering the temperature from 30 0C to 28 0C when the growth of the bacteria reaches a maximum. Jones et al. (Microbiol. Rev. 50(4):484-524 (1986)) review the role of temperature in ABE fermentation. They report that the solvent yields of three different solvent producing strains remains fairly constant at 31 % at 30 0C and 33 0C, but decreases to 23 to 25% at 37 0C. Similar results were reported for Clostridium acetobutylicum for which solvent yields decreased from 29% at 25 0C to 24% at 40 0C. In the latter case, the decrease in solvent yield was attributed to a decrease in acetone production while the yield of 1 -butanol was unaffected. However, Carnarius (U.S. Patent No. 2,198,104) reports that an increase in the butanol ratio is obtained in the ABE process by decreasing the temperature of the fermentation from 30 0C to 24 0C after 16 hours. However, the effect of temperature on the production of isobutanol by recombinant microbial hosts is not known in the art.
There is a need, therefore, for a cost-effective process for the production of isobutanol by fermentation that provides higher yields than processes known in the art. The present invention addresses this need through the discovery of a method for producing isobutanol by fermentation using a recombinant microbial host, which employs a decrease in temperature during fermentation, resulting in more robust tolerance of the production host to the isobutanol product. SUMMARY OF THE INVENTION
The invention provides a method for the production of isobutanol by fermentation using a recombinant microbial host, which employs a decrease in temperature during fermentation that results in more robust tolerance of the production host to the isobutanol product.
Accordingly, the invention provides a method for the production of isobutanol comprising: a) providing a recombinant microbial production host which produces isobutanol; b) seeding the production host of (a) into a fermentation medium comprising a fermentable carbon substrate to create a fermentation culture; c) growing the production host in the fermentation culture at a first temperature for a first period of time; d) lowering the temperature of the fermentation culture to a second temperature; and e) incubating the production host at the second temperature of step (d) for a second period of time; whereby isobutanol is produced. BRIEF DESCRIPTION OF THE FIGURES AND
SEQUENCE DESCRIPTIONS
The invention can be more fully understood from the following detailed description, figure, and the accompanying sequence descriptions, which form a part of this application. Figure 1 shows four different isobutanol biosynthetic pathways.
The steps labeled "a", "b", "c", "d", "e", T, "g", "h", "i", "j" and "k" represent the substrate to product conversions described below.
The following sequences conform with 37 C. F. R. 1.821 -1.825 ("Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures - the Sequence Rules") and are consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (1998) and the sequence listing requirements of the EPO and PCT (Rules 5.2 and 49.5(a-bis), and Section 208 and Annex C of the Administrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 CF. R. §1.822.
Table 1
Summary of Gene and Protein SEQ ID Numbers
Figure imgf000006_0001
Figure imgf000007_0001
Figure imgf000008_0001
Figure imgf000009_0001
SEQ ID NOs:11 -38, 40-69, 72-75, 85-138, 144, 145, 147-157, 159- 176 are the nucleotide sequences of oligonucleotide cloning, screening or sequencing primers used in the Examples described herein.
SEQ ID NO:39 is the nucleotide sequence of the cscBKA gene cluster described in Example 20.
SEQ ID NO:70 is the nucleotide sequence of the glucose isomerase promoter 1.6Gl described in Example 17.
SEQ ID NO:71 is the nucleotide sequence of the 1.5Gl promoter described in Example 17.
SEQ ID NO:76 is the nucleotide sequence of the GPD promoter described in Example 21.
SEQ ID NO:77 is the nucleotide sequence of the CYC1 terminator described in Example 21.
SEQ ID NO:79 is the nucleotide sequence of the FBA promoter described in Example 21. SEQ ID NO:81 is the nucleotide sequence of ADH1 promoter described in Example 21.
SEQW ID NO:82 is the nucleotide sequence of ADH1 terminator described in Example 21. SEQ ID NO:84 is the nucleotide sequence of GPM promoter described in Example 21.
SEQ ID NO:139 is the amino acid sequence of sucrose hydrolase (CscA).
SEQ ID NO:140 is the amino acid sequence of D-fructokinase (CscK).
SEQ ID NO:141 is the amino acid sequence of sucrose permease (CscB).
SEQ ID NO:142 is the nucleotide sequence of plasmid pFP988DssPspac described in Example 24. SEQ ID NO:143 is the nucleotide sequence of plasmid pFP988DssPgroE described in Example 24.
SEQ ID NO:146 is the nucleotide sequence of the pFP988Dss vector fragment described in Example 24.
SEQ ID NO:177 is the nucleotide sequence of the pFP988 integration vector described in Example 25.
SEQ ID NO:267 is the nucleotide sequence of plasmid pC194 described in Example 25.
DETAILED DESCRIPTION OF THE INVENTION The present invention relates to a method for the production of isobutanol using recombinant microorganisms that employs a decrease in temperature during fermentation, resulting in more robust tolerance of the production host to the isobutanol product and therefore a higher titer of isobutanol. The present invention meets a number of commercial and industrial needs. Butanol is an important industrial commodity chemical with a variety of applications, where its potential as a fuel or fuel additive is particularly significant. Although only a four-carbon alcohol, butanol has an energy content similar to that of gasoline and can be blended with any fossil fuel. Butanol is favored as a fuel or fuel additive as it yields only CO2 and little or no SOχ or NOχ when burned in the standard internal combustion engine. Additionally butanol is less corrosive than ethanol, the most preferred fuel additive to date.
In addition to its utility as a biofuel or fuel additive, butanol has the potential of impacting hydrogen distribution problems in the emerging fuel cell industry. Fuel cells today are plagued by safety concerns associated with hydrogen transport and distribution. Butanol can be easily reformed for its hydrogen content and can be distributed through existing gas stations in the purity required for either fuel cells or vehicles. Finally the present invention produces isobutanol from plant derived carbon sources, avoiding the negative environmental impact associated with standard petrochemical processes for butanol production.
The following definitions and abbreviations are to be used for the interpretation of the claims and the specification. As used herein, the terms "comprises," "comprising," "includes,"
"including," "has," "having," "contains" or "containing," or any other variation thereof, are intended to cover a non-exclusive inclusion. For example, a composition, a mixture, process, method, article, or apparatus that comprises a list of elements is not necessarily limited to only those elements but may include other elements not expressly listed or inherent to such composition, mixture, process, method, article, or apparatus. Further, unless expressly stated to the contrary, "or" refers to an inclusive or and not to an exclusive or. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).
Also, the indefinite articles "a" and "an" preceding an element or component of the invention are intended to be nonrestrictive regarding the number of instances (i.e. occurrences) of the element or component. Therefore "a" or "an" should be read to include one or at least one, and the singular word form of the element or component also includes the plural unless the number is obviously meant to be singular.
The term "invention" or "present invention" as used herein is a non- limiting term and is not intended to refer to any single embodiment of the particular invention but encompasses all possible embodiments as described in the specification and the claims.
As used herein, the term "about" modifying the quantity of an ingredient or reactant of the invention employed refers to variation in the numerical quantity that can occur, for example, through typical measuring and liquid handling procedures used for making concentrates or use solutions in the real world; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of the ingredients employed to make the compositions or carry out the methods; and the like. The term "about" also encompasses amounts that differ due to different equilibrium conditions for a composition resulting from a particular initial mixture. Whether or not modified by the term "about", the claims include equivalents to the quantities. In one embodiment, the term "about" means within 10% of the reported numerical value, preferably within 5% of the reported numerical value.
The term "isobutanol biosynthetic pathway" refers to an enzyme pathway to produce isobutanol.
The terms "acetolactate synthase" and "acetolactate synthetase" are used intechangeably herein to refer to an enzyme that catalyzes the conversion of pyruvate to acetolactate and CO2. Preferred acetolactate synthases are known by the EC number 2.2.1.6 9 (Enzyme Nomenclature 1992, Academic Press, San Diego). These enzymes are available from a number of sources, including, but not limited to, Bacillus subtilis (GenBank Nos: CAB15618 (SEQ ID NO:178), Z99122 (SEQ ID NO:78), NCBI (National Center for Biotechnology Information) amino acid sequence, NCBI nucleotide sequence, respectively), Klebsiella pneumoniae (GenBank Nos: AAA25079 (SEQ ID NO:2), M73842 (SEQ ID NO:1 )), and Lactococcus lactis (GenBank Nos: AAA25161 (SEQ ID NO:180), L16975 (SEQ ID NO:179)). The terms "acetohydroxy acid isomeroreductase" and
"acetohydroxy acid reductoisomerase" are used interchangeably herein to refer to an enzyme that catalyzes the conversion of acetolactate to 2,3- dihydroxyisovalerate using NADPH (reduced nicotinamide adenine dinucleotide phosphate) as an electron donor. Preferred acetohydroxy acid isomeroreductases are known by the EC number 1.1.1.86 and sequences are available from a vast array of microorganisms, including, but not limited to, Escherichia coli (GenBank Nos: NP_418222 (SEQ ID NO:4), NC_000913 (SEQ ID NO:3)), Saccharomyces cerevisiae (GenBank Nos: NP_013459 (SEQ ID NO:181 ), NC_001144 (SEQ ID
NO:80)), Methanococcus maripaludis (GenBank Nos: CAF30210 (SEQ ID NO:183), BX957220 (SEQ ID NO:182)), and Bacillus, subtilis (GenBank Nos: CAB14789 (SEQ ID NO:185), Z99118 (SEQ ID NO:184)).
The term "acetohydroxy acid dehydratase" refers to an enzyme that catalyzes the conversion of 2,3-dihydroxyisovalerate to α-ketoisovalerate. Preferred acetohydroxy acid dehydratases are known by the EC number 4.2.1.9. These enzymes are available from a vast array of microorganisms, including, but not limited to, E. coli (GenBank Nos: YP_026248 (SEQ ID NO:6), NC_000913 (SEQ ID NO:5)), S. cerevisiae (GenBank Nos: NP_012550 (SEQ ID NO:186), NC_001142 (SEQ ID NO:83)), M. maripaludis (GenBank Nos: CAF29874 (SEQ ID NO:188), BX957219 (SEQ ID NO:187)), and B. subtilis (GenBank Nos: CAB14105 (SEQ ID NO:190), Z99115 (SEQ ID NO:189)).
The term "branched-chain α-keto acid decarboxylase" refers to an enzyme that catalyzes the conversion of α-ketoisovalerate to isobutyraldehyde and CO2. Preferred branched-chain α-keto acid decarboxylases are known by the EC number 4.1.1.72 and are available from a number of sources, including, but not limited to, Lactococcus lactis (GenBank Nos: AAS49166 (SEQ ID NO:193), AY548760 (SEQ ID NO:192); CAG34226 (SEQ ID NO:8), AJ746364 (SEQ ID NO:191 ),
Salmonella typhimurium (GenBank Nos: NP_461346 (SEQ ID NO:195), NC_003197 (SEQ ID NO:194)), and Clostridium acetobutylicum (GenBank Nos: NPJ49189 (SEQ ID NO:197), NC_001988 (SEQ ID NO:196)). The term "branched-chain alcohol dehydrogenase" refers to an enzyme that catalyzes the conversion of isobutyraldehyde to isobutanol. Preferred branched-chain alcohol dehydrogenases are known by the EC number 1.1.1.265, but may also be classified under other alcohol dehydrogenases (specifically, EC 1.1.1.1 or 1.1.1.2). These enzymes utilize NADH (reduced nicotinamide adenine dinucleotide) and/or NADPH as electron donor and are available from a number of sources, including, but not limited to, S. cerevisiae (GenBank Nos: NP_010656 (SEQ ID NO:199), NC_001136 (SEQ ID NO:198); NP_014051 (SEQ ID NO:201 ) NC_001145 (SEQ ID NO:200)), E. coli (GenBank Nos: NP_417484 (SEQ ID NO:10), NC_000913 (SEQ ID NO:9)), and C. acetobutylicum (GenBank Nos: NP_349892 (SEQ ID NO:203), NC_003030 (SEQ ID NO:202); NP_349891 (SEQ ID NO:204), NC_003030 (SEQ ID NO:158)).
The term "branched-chain keto acid dehydrogenase" refers to an enzyme that catalyzes the conversion of α-ketoisovalerate to isobutyryl- CoA (isobutyryl-coenzyme A), using NAD+ (nicotinamide adenine dinucleotide) as electron acceptor. Preferred branched-chain keto acid dehydrogenases are known by the EC number 1.2.4.4. These branched- chain keto acid dehydrogenases are comprised of four subunits and sequences from all subunits are available from a vast array of microorganisms, including, but not limited to, B. subtilis (GenBank Nos: CAB14336 (SEQ ID NO:206), Z99116 (SEQ ID NO:205); CAB14335 (SEQ ID NO:208), Z99116 (SEQ ID NO:207); CAB14334 (SEQ ID NO:210), Z99116 (SEQ ID NO:209); and CAB14337 (SEQ ID NO:212), Z99116 (SEQ ID NO:211 )) and Pseudomonas putida (GenBank Nos: AAA65614 (SEQ ID NO:214), M57613 (SEQ ID NO:213); AAA65615 (SEQ ID NO:216), M57613 (SEQ ID NO:215); AAA65617 (SEQ ID NO:218), M57613 (SEQ ID NO:217); and AAA65618 (SEQ ID NO:220), M57613 (SEQ ID NO:219)). The term "acylating aldehyde dehydrogenase" refers to an enzyme that catalyzes the conversion of isobutyryl-CoA to isobutyraldehyde, using either NADH or NADPH as electron donor. Preferred acylating aldehyde dehydrogenases are known by the EC numbers 1.2.1.10 and 1.2.1.57. These enzymes are available from multiple sources, including, but not limited to, Clostridium beijerinckii (GenBank Nos: AAD31841 (SEQ ID
NO:222), AF157306 (SEQ ID NO:221 )), C. acetobutylicum (GenBank Nos: NP_149325 (SEQ ID NO:224), NC_001988 (SEQ ID NO:223); NPJ49199 (SEQ ID NO:226), NC_001988 (SEQ ID NO:225)), P. putida (GenBank Nos: AAA89106 (SEQ ID NO:228), U13232 (SEQ ID NO:227)), and Thermus thermophilus (GenBank Nos: YP_145486 (SEQ ID NO:230), NC_006461 (SEQ ID NO:229)).
The term "transaminase" refers to an enzyme that catalyzes the conversion of α-ketoisovalerate to L-valine, using either alanine or glutamate as amine donor. Preferred transaminases are known by the EC numbers 2.6.1.42 and 2.6.1.66. These enzymes are available from a number of sources. Examples of sources for alanine-dependent enzymes include, but are not limited to, E. coli (GenBank Nos: YP_026231 (SEQ ID NO:232), NC_000913 (SEQ ID NO:231 )) and Bacillus licheniformis (GenBank Nos: YP_093743 (SEQ ID NO:234), NC_006322 (SEQ ID NO:233)). Examples of sources for glutamate-dependent enzymes include, but are not limited to, E. coli (GenBank Nos: YP_026247 (SEQ ID NO:236), NC_000913 (SEQ ID NO:235)), S. cerevisiae (GenBank Nos: NP_012682 (SEQ ID NO:238), NC_001142 (SEQ ID NO:237)) and Methanobacterium thermoautotrophicum (GenBank Nos: NP_276546 (SEQ ID NO:240), NC_000916 (SEQ ID NO:239)).
The term "valine dehydrogenase" refers to an enzyme that catalyzes the conversion of α-ketoisovalerate to L-valine, using NAD(P)H as electron donor and ammonia as amine donor. Preferred valine dehydrogenases are known by the EC numbers 1.4.1.8 and 1.4.1.9 and are available from a number of sources, including, but not limited to, Streptomyces coelicolor (GenBank Nos: NP_628270 (SEQ ID NO:242), NC_003888 (SEQ ID NO:241 )) and B. subtilis (GenBank Nos: CAB14339 (SEQ ID NO:244), Z99116 (SEQ ID NO:243)).
The term "valine decarboxylase" refers to an enzyme that catalyzes the conversion of L-valine to isobutylamine and CO2. Preferred valine decarboxylases are known by the EC number 4.1.1.14. These enzymes are found in Streptomycetes, such as for example, Streptomyces viridifaciens (GenBank Nos: AAN 10242 (SEQ ID NO:246), AY116644 (SEQ ID NO:245)).
The term "omega transaminase" refers to an enzyme that catalyzes the conversion of isobutylamine to isobutyraldehyde using a suitable amino acid as amine donor. Preferred omega transaminases are known by the EC number 2.6.1.18 and are available from a number of sources, including, but not limited to, Alcaligenes denitrificans (AAP92672 (SEQ ID NO:248), AY330220 (SEQ ID NO:247)), Ralstonia eutropha (GenBank Nos: YP_294474 (SEQ ID NO:250), NC_007347 (SEQ ID NO:249)), Shewanella oneidensis (GenBank Nos: NP_719046 (SEQ ID NO:252), NC_004347 (SEQ ID NO:251 )), and P. putida (GenBank Nos: AAN66223 (SEQ ID NO:254), AE016776 (SEQ ID NO:253)).
The term "isobutyryl-CoA mutase" refers to an enzyme that catalyzes the conversion of butyryl-CoA to isobutyryl-CoA. This enzyme uses coenzyme B12 as cofactor. Preferred isobutyryl-CoA mutases are known by the EC number 5.4.99.13. These enzymes are found in a number of Streptomycetes, including, but not limited to, Streptomyces cinnamonensis (GenBank Nos: AAC08713 (SEQ ID NO:256), U67612 (SEQ ID NO:255); CAB59633 (SEQ ID NO:258), AJ246005 (SEQ ID NO:257)), S. coelicolor (GenBank Nos: CAB70645 (SEQ ID NO:260), AL939123 (SEQ ID NO:259); CAB92663 (SEQ ID NO:262), AL939121 (SEQ ID NO:261 )), and Streptomyces avermitilis (GenBank Nos: NP_824008 (SEQ ID NO:264), NC_003155 (SEQ ID NO:263); NP_824637 (SEQ ID NO:266), NC_003155 (SEQ ID NO:265)).
The term "a facultative anaerobe" refers to a microorganism that can grow in both aerobic and anaerobic environments.
The term "carbon substrate" or "fermentable carbon substrate" refers to a carbon source capable of being metabolized by host organisms disclosed herein and particularly carbon sources selected from the group consisting of monosaccharides, oligosaccharides, polysaccharides, and one-carbon substrates or mixtures thereof.
The term "gene" refers to a nucleic acid fragment that is capable of being expressed as a specific protein, optionally including regulatory sequences preceding (5' non-coding sequences) and following (3' non- coding sequences) the coding sequence. "Native gene" refers to a gene as found in nature with its own regulatory sequences. "Chimeric gene" refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. "Endogenous gene" refers to a native gene in its natural location in the genome of an organism. A
"foreign gene" or "heterologous gene" refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non- native organism, or chimeric genes. A "transgene" is a gene that has been introduced into the genome by a transformation procedure.
As used herein, an "isolated nucleic acid fragment" or "isolated nucleic acid molecule" or "genetic construct" will be used interchangeably and will mean a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. An isolated nucleic acid fragment in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA or synthetic DNA.
A nucleic acid fragment is "hybhdizable" to another nucleic acid fragment, such as a cDNA, genomic DNA, or RNA molecule, when a single-stranded form of the nucleic acid fragment can anneal to the other nucleic acid fragment under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory: Cold Spring Harbor, NY (1989), particularly Chapter 11 and Table 11.1 therein (entirely incorporated herein by reference). The conditions of temperature and ionic strength determine the "stringency" of the hybridization. Stringency conditions can be adjusted to screen for moderately similar fragments (such as homologous sequences from distantly related organisms), to highly similar fragments (such as genes that duplicate functional enzymes from closely related organisms). Post-hybridization washes determine stringency conditions. One set of preferred conditions uses a series of washes starting with 6X SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2X SSC, 0.5% SDS at 45 0C for 30 min, and then repeated twice with 0.2X SSC, 0.5% SDS at 50 0C for 30 min. A more preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2X SSC, 0.5% SDS was increased to 60 0C. Another preferred set of highly stringent conditions uses two final washes in 0.1X SSC, 0.1 % SDS at 65 0C. An additional set of stringent conditions include hybridization at 0.1X SSC, 0.1 % SDS, 65 0C and washes with 2X SSC, 0.1 % SDS followed by 0.1 X SSC, 0.1 % SDS, for example.
Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra, 9.50-9.51 ). For hybridizations with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra, 11.7-11.8). In one embodiment the length for a hybridizable nucleic acid is at least about 10 nucleotides. Preferably a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; more preferably at least about 20 nucleotides; and most preferably the length is at least about 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be adjusted as necessary according to factors such as length of the probe.
A "substantial portion" of an amino acid or nucleotide sequence is that portion comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Altschul, S. F., et al., J. MoI. Biol., 215:403-410 (1993)). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a "substantial portion" of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence. The instant specification teaches the complete amino acid and nucleotide sequence encoding particular fungal proteins. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above. The term "complementary" is used to describe the relationship between nucleotide bases that are capable of hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine.
The terms "homology" and "homologous" are used interchangeably herein. They refer to nucleic acid fragments wherein changes in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate gene expression or produce a certain phenotype. These terms also refer to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotides that do not substantially alter the functional properties of the resulting nucleic acid fragment relative to the initial, unmodified fragment. It is therefore understood, as those skilled in the art will appreciate, that the invention encompasses more than the specific exemplary sequences. Moreover, the skilled artisan recognizes that homologous nucleic acid sequences encompassed by this invention are also defined by their ability to hybridize, under moderately stringent conditions (e.g., 0.5 X SSC, 0.1 % SDS, 60 0C) with the sequences exemplified herein, or to any portion of the nucleotide sequences disclosed herein and which are functionally equivalent to any of the nucleic acid sequences disclosed herein.
"Codon degeneracy" refers to the nature in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide. The skilled artisan is well aware of the "codon-bias" exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.
The term "percent identity", as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, "identity" also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. "Identity" and "similarity" can be readily calculated by known methods, including but not limited to those described in: 1.) Computational Molecular Biology (Lesk, A. M., Ed.) Oxford University: NY (1988); 2.) Biocomputinq: Informatics and Genome Projects (Smith, D. W., Ed.) Academic: NY (1993); 3.) Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., Eds.) Humania: NJ (1994); 4.) Sequence Analysis in Molecular Biology (von Heinje, G., Ed.) Academic (1987); and 5.) Sequence Analysis Primer (Ghbskov, M. and Devereux, J., Eds.) Stockton: NY (1991 ). Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using the MegAlign™ program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wl). Multiple alignment of the sequences is performed using the "Clustal method of alignment" which encompasses several varieties of the algorithm including the "Clustal V method of alignment" corresponding to the alignment method labeled Clustal V (described by Higgins and Sharp, CABIOS. 5:151 -153 (1989); Higgins, D.G. et al., Comput. Appl. Biosci., 8:189-191 (1992)) and found in the MegAlign™ program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.). For multiple alignments, the default values correspond to GAP PENALTY=I O and GAP LENGTH PENALTY=I O. Default parameters for pairwise alignments and calculation of percent identity of protein sequences using the Clustal method are KTUPLE=I , GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. For nucleic acids these parameters are KTUPLE=2, GAP PENALTY=5, WINDOW=4 and DIAGONALS SAVED=4. After alignment of the sequences using the Clustal V program, it is possible to obtain a "percent identity" by viewing the "sequence distances" table in the same program. Additionally the "Clustal W method of alignment" is available and corresponds to the alignment method labeled Clustal W (described by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins, D.G. et al., Comput. Appl. Biosci. 8:189-191 (1992)) and found in the MegAlign™ v6.1 program of the
LASERGENE bioinformatics computing suite (DNASTAR Inc.). Default parameters for multiple alignment (GAP PENALTY=IO, GAP LENGTH PENALTY=0.2, Delay Divergen Seqs(%)=30, DNA Transition Weight=0.5, Protein Weight Matrix=Gonnet Series, DNA Weight Mathx=IUB ). After alignment of the sequences using the Clustal W program, it is possible to obtain a "percent identity" by viewing the "sequence distances" table in the same program. It is well understood by one skilled in the art that many levels of sequence identity are useful in identifying polypeptides, from other species, wherein such polypeptides have the same or similar function or activity. Useful examples of percent identities include, but are not limited to: 24%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, or any integer percentage from 24% to 100% may be useful in describing the present invention, such as 25%, 26%, 27%, 28%, 29%, 30%, 31 %, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41 %, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%. Suitable nucleic acid fragments not only have the above homologies but typically encode a polypeptide having at least 50 amino acids, preferably at least 100 amino acids, more preferably at least 150 amino acids, still more preferably at least 200 amino acids, and most preferably at least 250 amino acids.
The term "sequence analysis software" refers to any computer algorithm or software program that is useful for the analysis of nucleotide or amino acid sequences. "Sequence analysis software" may be commercially available or independently developed. Typical sequence analysis software will include, but is not limited to: 1.) the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wl); 2.) BLASTP, BLASTN, BLASTX (Altschul et al., J. MoI. Biol., 215:403-410 (1990)); 3.) DNASTAR (DNASTAR, Inc.
Madison, Wl); 4.) Sequencher (Gene Codes Corporation, Ann Arbor, Ml); and 5.) the FASTA program incorporating the Smith-Waterman algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111 -20. Editor(s): Suhai, Sandor. Plenum: New York, NY). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the "default values" of the program referenced, unless otherwise specified. As used herein "default values" will mean any set of values or parameters that originally load with the software when first initialized.
As used herein the term "coding sequence" refers to a DNA sequence that codes for a specific amino acid sequence. "Suitable regulatory sequences" refer to nucleotide sequences located upstream (5' non-coding sequences), within, or downstream (3' non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing site, effector binding site and stem-loop structure.
The term "promoter" refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3' to a promoter sequence. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters which cause a gene to be expressed in most cell types at most times are commonly referred to as "constitutive promoters". It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.
The term "operably linked" refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of effecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.
The term "expression", as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment disclosed herein. Expression may also refer to translation of mRNA into a polypeptide.
As used herein the term "transformation" refers to the transfer of a nucleic acid fragment into a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as "transgenic" or "recombinant" or "transformed" organisms.
The terms "plasmid" and "vector" refer to an extra chromosomal element often carrying genes which are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA moledules. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3' untranslated sequence into a cell. "Transformation vector" refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitates transformation of a particular host cell.
As used herein the term "codon degeneracy" refers to the nature in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide. The skilled artisan is well aware of the "codon-bias" exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.
The term "codon-optimized" as it refers to genes or coding regions of nucleic acid molecules for transformation of various hosts, refers to the alteration of codons in the gene or coding regions of the nucleic acid molecules to reflect the typical codon usage of the host organism without altering the polypeptide encoded by the DNA. Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1989) (hereinafter "Maniatis"); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1984); and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc, and Wiley-lnterscience (1987). lsobutanol Biosynthetic Pathways
Carbohydrate utilizing microorganisms employ the Embden- Meyerhof-Parnas (EMP) pathway, the Entner-Doudoroff pathway and the pentose phosphate cycle as the central, metabolic routes to provide energy and cellular precursors for growth and maintenance. These pathways have in common the intermediate glyceraldehyde-3-phosphate and, ultimately, pyruvate is formed directly or in combination with the EMP pathway. Subsequently, pyruvate is transformed to acetyl-coenzyme A (acetyl-CoA) via a variety of means. Acetyl-CoA serves as a key intermediate, for example, in generating fatty acids, amino acids and secondary metabolites. The combined reactions of sugar conversion to pyruvate produce energy (e.g. adenosine-5'-triphosphate, ATP) and reducing equivalents (e.g. reduced nicotinamide adenine dinucleotide, NADH, and reduced nicotinamide adenine dinucleotide phosphate, NADPH). NADH and NADPH must be recycled to their oxidized forms (NAD+ and NADP+, respectively). In the presence of inorganic electron acceptors (e.g. O2, NO3" and SO4 2"), the reducing equivalents may be used to augment the energy pool; alternatively, a reduced carbon by-product may be formed. As described by Donaldson et al., supra, isobutanol can be produced from carbohydrate sources by recombinant microorganisms comprising one of four complete isobutanol biosynthetic pathways, as shown in Figure 1.
Three of the pathways comprise conversion of pyruvate to isobutanol via a series of enzymatic steps. The preferred isobutanol pathway (Figure 1 , steps a to e), comprises the following substrate to product conversions: a) pyruvate to acetolactate, as catalyzed for example by acetolactate synthase, b) acetolactate to 2,3-dihydroxyisovalerate, as catalyzed for example by acetohydroxy acid isomeroreductase, c) 2,3-dihydroxyisovalerate to α-ketoisovalerate, as catalyzed for example by acetohydroxy acid dehydratase, d) α-ketoisovalerate to isobutyraldehyde, as catalyzed for example by a branched-chain keto acid decarboxylase, and e) isobutyraldehyde to isobutanol, as catalyzed for example by, a branched-chain alcohol dehydrogenase.
This pathway combines enzymes known to be involved in well- characterized pathways for valine biosynthesis (pyruvate to α- ketoisovalerate) and valine catabolism (α-ketoisovalerate to isobutanol). Since many valine biosynthetic enzymes also catalyze analogous reactions in the isoleucine biosynthetic pathway, substrate specificity is a major consideration in selecting the gene sources. For this reason, the primary genes of interest for the acetolactate synthase enzyme are those from Bacillus (alsS) and Klebsiella (budB). These particular acetolactate synthases are known to participate in butanediol fermentation in these organisms and show increased affinity for pyruvate over ketobutyrate (Gollop et al., J. Bacteriol. 172(6):3444-3449 (1990); Holtzclaw et al., J. Bacteriol. 121 (3):917-922 (1975)). The second and third pathway steps are catalyzed by acetohydroxy acid reductoisomerase and dehydratase, respectively. These enzymes have been characterized from a number of sources, such as for example, E. coli (Chunduru et al., Biochemistry 28(2):486-493 (1989); Flint et al., J. Biol. Chem. 268(29):14732-14742 (1993)). The final two steps of the preferred isobutanol pathway are known to occur in yeast, which can use valine as a nitrogen source and, in the process, secrete isobutanol. α-Ketoisovalerate can be converted to isobutyraldehyde by a number of keto acid decarboxylase enzymes, such as for example pyruvate decarboxylase. To prevent misdirection of pyruvate away from isobutanol production, a decarboxylase with decreased affinity for pyruvate is desired. So far, there are two such enzymes known in the art (Smit et al., Appl. Environ. Microbiol. 71 (1 ):303- 311 (2005); de Ia Plaza et al., FEMS Microbiol. Lett. 238(2):367-374 (2004)). Both enzymes are from strains of Lactococcus lactis and have a 50-200-fold preference for ketoisovalerate over pyruvate. Finally, a number of aldehyde reductases have been identified in yeast, many with overlapping substrate specificity. Those known to prefer branched-chain substrates over acetaldehyde include, but are not limited to, alcohol dehydrogenase Vl (ADH6) and Ypri p (Larroy et al., Biochem. J. 361 (Pt 1 ):163-172 (2002); Ford et al., Yeast 19(12):1087-1096 (2002)), both of which use NADPH as electron donor. An NADPH-dependent reductase, YqhD, active with branched-chain substrates has also been recently identified in E. coli (Sulzenbacher et al., J. MoI. Biol. 342(2):489-502 (2004)).
Pathway steps. a) Pyruvate to acetolactate, is catalyzed by acetolactate synthase. The skilled person will appreciate that polypeptides having acetolactate synthase activity isolated from a variety of sources will be useful in the present invention independent of sequence homology.
Example of suitable acetolactate synthase enzymes are available from a number of sources, for example, Bacillus subtilis (GenBank Nos: CAB15618 (SEQ ID NO:178), Z99122 (SEQ ID NO:78), NCBI (National Center for Biotechnology Information) amino acid sequence, NCBI nucleotide sequence, respectively), Klebsiella pneumoniae (GenBank Nos: AAA25079 (SEQ ID NO:2), M73842 (SEQ ID NO:1 )), and Lactococcus lactis (GenBank Nos: AAA25161 (SEQ ID NO:180), L16975 (SEQ ID NO:179)). Preferred acetolactate synthase enzymes are those that have at least 80% - 85% identity to SEQ ID NO:2, SEQ ID NO:178, and SEQ ID: 180 where at least 85% - 90% identity is more preferred and where at least 95% identity based on the Clustal W method of alignment using the default parameters of GAP PENALTY=I O, GAP LENGTH PENALTY=O.1 , and Gonnet 250 series of protein weight matrix, is most preferred. b) Acetolactate to 2,3-dihydroxyisovalerate, is catalyzed by acetohydroxy acid isomeroreductase. The skilled person will appreciate that polypeptides having acetohydroxy acid isomeroreductase activity isolated from a variety of sources will be useful in the present invention independent of sequence homology. Example of suitable acetohydroxy acid isomeroreductase enzymes are available from a number of sources, for example, Escherichia coli (GenBank Nos: NP_418222 (SEQ ID NO:4), NC_000913 (SEQ ID NO:3)), Saccharomyces cerevisiae (GenBank Nos: NP_013459 (SEQ ID NO:181 ), NC_001144 (SEQ ID NO:80)), Methanococcus maripaludis (GenBank Nos: CAF30210 (SEQ ID NO:183), BX957220 (SEQ ID NO:182)), and Bacillus, subtilis (GenBank Nos: CAB14789 (SEQ ID NO:185), Z99118 (SEQ ID NO:184)). Preferred acetohydroxy acid isomeroreductase enzymes are those that have at least 80% - 85% identity to SEQ ID NO:43, SEQ ID NO:181 , SEQ ID NO:183, and SEQ ID NO:185, where at least 85% - 90% identity is more preferred and where at least 95% identity based on the Clustal W method of alignment using the default parameters of GAP PENALTY=I O, GAP LENGTH PENALTY=O.1 , and Gonnet 250 series of protein weight matrix, is most preferred. c) 2,3-dihydroxyisovalerate to α-ketoisovalerate, as catalyzed for example by acetohydroxy acid dehydratase. The skilled person will appreciate that polypeptides having acetohydroxy acid dehydratase activity isolated from a variety of sources will be useful in the present invention independent of sequence homology. Example of suitable acetohydroxy acid dehydratase enzymes are available from a number of sources, for example, E. coli (GenBank Nos: YP_026248 (SEQ ID NO:6), NC_000913 (SEQ ID NO:5)), S. cerevisiae (GenBank Nos: NP_012550 (SEQ ID NO:186), NC_001142 (SEQ ID NO:83)), M. maripaludis (GenBank Nos: CAF29874 (SEQ ID NO:188), BX957219 (SEQ ID NO:187)), and B. subtilis (GenBank Nos: CAB14105 (SEQ ID NO:190), Z99115 (SEQ ID NO:189)). Preferred acetohydroxy acid dehydratase enzymes are those that have at least 80% - 85% identity to SEQ ID NO:6, SEQ ID NO:186, SEQ ID NO:188, and SEQ ID NO:190, where at least 85% - 90% identity is more preferred and where at least 95% identity based on the Clustal W method of alignment using the default parameters Of GAP PENALTY=I O, GAP LENGTH PENALTY=0.1 , and Gonnet 250 series of protein weight matrix, is most preferred. d) α-ketoisovalerate to isobutyraldehyde, as catalyzed for example by a branched-chain keto acid decarboxylase. The skilled person will appreciate that polypeptides having branched-chain keto acid decarboxylase activity isolated from a variety of sources will be useful in the present invention independent of sequence homology. Example of suitable branched-chain keto acid decarboxylase enzymes are available from a number of sources, for example, Lactococcus lactis (GenBank Nos: AAS49166 (SEQ ID NO:193), AY548760 (SEQ ID NO:192); CAG34226 (SEQ ID NO:8), AJ746364 (SEQ ID NO:191 ), Salmonella typhimurium (GenBank Nos: NP_461346 (SEQ ID NO:195), NC_003197 (SEQ ID NO:194)), and Clostridium acetobutylicum (GenBank Nos: NPJ49189 (SEQ ID NO:197), NC_001988 (SEQ ID NO:196)).
Preferred branched-chain keto acid decarboxylase enzymes are those that have at least 80% - 85% identity to SEQ ID NO:8, SEQ ID NO:193, SEQ
ID NO:195, and SEQ ID NO:197, where at least 85% - 90% identity is more preferred and where at least 95% identity based on the Clustal W method of alignment using the default parameters of GAP PENALTY=I 0, GAP LENGTH PENALTY=O.1 , and Gonnet 250 series of protein weight matrix, is most preferred. e) Isobutyraldehyde to isobutanol, as catalyzed for example by, a branched-chain alcohol dehydrogenase. The skilled person will appreciate that polypeptides having branched-chain alcohol dehydrogenase activity isolated from a variety of sources will be useful in the present invention independent of sequence homology. Example of suitable branched-chain alcohol dehydrogenase enzymes are available from a number of sources, for example, S. cerevisiae (GenBank Nos: NP_010656 (SEQ ID NO:199), NC_001136 (SEQ ID NO:198); NP_014051 (SEQ ID NO:201 ) NC_001145 (SEQ ID NO:200)), E. coli (GenBank Nos: NP_417484 (SEQ ID NO:10), NC_000913 (SEQ ID NO:9)), and C. acetobutylicum (GenBank Nos: NP_349892 (SEQ ID NO:203), NC_003030 (SEQ ID NO:202); NP_349891 (SEQ ID NO:204), NC_003030 (SEQ ID NO:158)). Preferred branched-chain alcohol dehydrogenase enzymes are those that have at least 80% - 85% identity to SEQ ID NO:10, SEQ ID NO:199, SEQ ID NO:201 , SEQ ID NO:203, and SEQ ID NO:204.where at least 85% - 90% identity is more preferred and where at least 95% identity based on the Clustal W method of alignment using the default parameters of GAP PENALTY=I O, GAP LENGTH PENALTY=O.1 , and Gonnet 250 series of protein weight matrix, is most preferred.
Additional pathways are discussed below and in commonly owned and copending US 11/586315, incorporated herein by reference. Another pathway for converting pyruvate to isobutanol comprises the following substrate to product conversions (Figure 1 , steps a,b,c,f,g,e): a) pyruvate to acetolactate, as catalyzed for example by acetolactate synthase, b) acetolactate to 2,3-dihydroxyisovalerate, as catalyzed for example by acetohydroxy acid isomeroreductase, c) 2,3-dihydroxyisovalerate to α-ketoisovalerate, as catalyzed for example by acetohydroxy acid dehydratase, f) α-ketoisovalerate to isobutyryl-CoA, as catalyzed for example by a branched-chain keto acid dehydrogenase, g) isobutyryl-CoA to isobutyraldehyde, as catalyzed for example by an acylating aldehyde dehydrogenase, and e) isobutyraldehyde to isobutanol, as catalyzed for example by, a branched-chain alcohol dehydrogenase.
The first three steps in this pathway (a,b,c) are the same as those described above. The α-ketoisovalerate is converted to isobutyryl-CoA by the action of a branched-chain keto acid dehydrogenase. While yeast can only use valine as a nitrogen source, many other organisms (both eukaryotes and prokaryotes) can use valine as the carbon source as well. These organisms have branched-chain keto acid dehydrogenase (Sokatch et al. J. Bacteriol. 148(2):647-652 (1981 )), which generates isobutyryl- CoA. Isobutyryl-CoA may be converted to isobutyraldehyde by an acylating aldehyde dehydrogenase. Dehydrogenases active with the branched-chain substrate have been described, but not cloned, in Leuconostoc and Propionibacteήum (Kazahaya et al., J. Gen. Appl. Microbiol. 18:43-55 (1972); Hosoi et al., J. Ferment. Technol. 57:418-427 (1979)). However, it is also possible that acylating aldehyde dehydrogenases known to function with straight-chain acyl-CoAs (i.e. butyryl-CoA), may also work with isobutyryl-CoA. The isobutyraldehyde is then converted to isobutanol by a branched-chain alcohol dehydrogenase, as described above for the first pathway.
Another pathway for converting pyruvate to isobutanol comprises the following substrate to product conversions (Figure 1 , steps a,b,c,h,i,j,e): a) pyruvate to acetolactate, as catalyzed for example by acetolactate synthase, b) acetolactate to 2,3-dihydroxyisovalerate, as catalyzed for example by acetohydroxy acid isomeroreductase, c) 2,3-dihydroxyisovalerate to α-ketoisovalerate, as catalyzed for example by acetohydroxy acid dehydratase, h) α-ketoisovalerate to valine, as catalyzed for example by valine dehydrogenase or transaminase, i) valine to isobutylamine, as catalyzed for example by valine decarboxylase, j) isobutylamine to isobutyraldehyde, as catalyzed for example by omega transaminase, and e) isobutyraldehyde to isobutanol, as catalyzed for example by, a branched-chain alcohol dehydrogenase.
The first three steps in this pathway (a,b,c) are the same as those described above. This pathway requires the addition of a valine dehydrogenase or a suitable transaminase. Valine (and or leucine) dehydrogenase catalyzes reductive amination and uses ammonia; Km values for ammonia are in the millimolar range (Priestly et al., Biochem J. 261 (3):853-861 (1989); Vancura et al., J. Gen. Microbiol. 134(12):3213- 3219 (1988) Zink et al., Arch. Biochem. Biophys. 99:72-77 (1962); Sekimoto et al. J. Biochem (Japan) 116(1 ):176-182 (1994)). Transaminases typically use either glutamate or alanine as amino donors and have been characterized from a number of organisms (Lee-Peng et al,. J. Bacteriol. 139(2):339-345 (1979); Berg et al., J. Bacteriol. 155(3): 1009-1014 (1983)). An alanine-specific enzyme may be desirable, since the generation of pyruvate from this step could be coupled to the consumption of pyruvate later in the pathway when the amine group is removed (see below). The next step is decarboxylation of valine, a reaction that occurs in valanimycin biosynthesis in Streptomyces (Garg et al., MoI. Microbiol. 46(2):505-517 (2002)). The resulting isobutylamine may be converted to isobutyraldehyde in a pyridoxal 5'-phosphate- dependent reaction by, for example, an enzyme of the omega- aminotransferase family. Such an enzyme from Vibrio fluvialis has demonstrated activity with isobutylamine (Shin et al., Biotechnol. Bioeng. 65(2):206-211 (1999)). Another omega-am inotransferase from Alcaligenes denitrificans has been cloned and has some activity with butylamine (Yun et al., Appl. Environ. Microbiol. 70(4):2529-2534 (2004)). In this direction, these enzymes use pyruvate as the amino acceptor, yielding alanine. As mentioned above, adverse affects on the pyruvate pool may be offset by using a pyruvate-producing transaminase earlier in the pathway. The isobutyraldehyde is then converted to isobutanol by a branched-chain alcohol dehydrogenase, as described above for the first pathway. The fourth isobutanol biosynthetic pathway comprises the substrate to product conversions shown as steps k,g,e in Figure 1. A number of organisms are known to produce butyrate and/or butanol via a butyryl-CoA intermediate (Dϋrre et al., FEMS Microbiol. Rev. 17(3):251-262 (1995); Abbad-Andaloussi et al., Microbiology 142(5): 1149-1158 (1996)). Isobutanol production may be engineered in these organisms by addition of a mutase able to convert butyryl-CoA to isobutyryl-CoA (Figure 1 , step k). Genes for both subunits of isobutyryl-CoA mutase, a coenzyme B12- dependent enzyme, have been cloned from a Streptomycete (Ratnatilleke et al., J. Biol. Chem. 274(44):31679-31685 (1999)). The isobutyryl-CoA is converted to isobutyraldehyde (step g in Figure 1 ), which is converted to isobutanol (step e in Figure 1 ).
Thus, in providing multiple recombinant pathways from pyruvate to isobutanol, there exist a number of choices to fulfill the individual conversion steps, and the person of skill in the art will be able to utilize publicly available sequences to construct the relevant pathways. A listing of a representative number of genes known in the art and useful in the construction of isobutanol biosynthetic pathways are listed below in Table 2. Table 2
Sources of lsobuatnol Biosynthetic Pathway Genes
Figure imgf000033_0001
Figure imgf000034_0001
Figure imgf000035_0001
Figure imgf000036_0001
Microbial Hosts for lsobutanol Production
Microbial hosts for isobutanol production may be selected from bacteria, cyanobacteria, filamentous fungi and yeasts. The microbial host used for isobutanol production is preferably tolerant to isobutanol so that the yield is not limited by isobutanol toxicity. Microbes that are metabolically active at high titer levels of isobutanol are not well known in the art. Although 1-butanol-tolerant mutants have been isolated from solventogenic Clostridia, little information is available concerning the butanol tolerance of other potentially useful bacterial strains. Most of the studies on the comparison of alcohol tolerance in bacteria suggest that 1 - butanol is more toxic than ethanol (de Cavalho et al., Microsc. Res. Tech. 64:215-22 (2004) and Kabelitz et al., FEMS Microbiol. Lett. 220:223-227 (2003)). Tomas et al. {J. Bacteriol. 186:2006-2018 (2004)) report that the yield of 1 -butanol during fermentation in Clostridium acetobutylicum may be limited by 1 -butanol toxicity. The primary effect of 1 -butanol on Clostridium acetobutylicum is disruption of membrane functions (Hermann et al., Appl. Environ. Microbiol. 50:1238-1243 (1985)).
The microbial hosts selected for the production of isobutanol are preferably tolerant to isobutanol and should be able to convert carbohydrates to isobutanol. The criteria for selection of suitable microbial hosts include the following: intrinsic tolerance to isobutanol, high rate of glucose utilization, availability of genetic tools for gene manipulation, and the ability to generate stable chromosomal alterations. Suitable host strains with a tolerance for isobutanol may be identified by screening based on the intrinsic tolerance of the strain. The intrinsic tolerance of microbes to isobutanol may be measured by determining the concentration of isobutanol that is responsible for 50% inhibition of the growth rate (IC50) when grown in a minimal medium. The IC50 values may be determined using methods known in the art. For example, the microbes of interest may be grown in the presence of various amounts of isobutanol and the growth rate monitored by measuring the optical density at 600 nanometers. The doubling time may be calculated from the logarithmic part of the growth curve and used as a measure of the growth rate. The concentration of isobutanol that produces 50% inhibition of growth may be determined from a graph of the percent inhibition of growth versus the isobutanol concentration. Preferably, the host strain should have an IC50 for isobutanol of greater than about 0.5%. The microbial host for isobutanol production should also utilize glucose at a high rate. Most microbes are capable of utilizing carbohydrates. However, certain environmental microbes cannot utilize carbohydrates to high efficiency, and therefore would not be suitable hosts. The ability to genetically modify the host is essential for the production of any recombinant microorganism. The mode of gene transfer technology may be by electroporation, conjugation, transduction or natural transformation. A broad range of host conjugative plasmids and drug resistance markers are available. The cloning vectors are tailored to the host organisms based on the nature of antibiotic resistance markers that can function in that host.
The microbial host also has to be manipulated in order to inactivate competing pathways for carbon flow by deleting various genes. This requires the availability of either transposons to direct inactivation or chromosomal integration vectors. Additionally, the production host should be amenable to chemical mutagenesis so that mutations to improve intrinsic isobutanol tolerance may be obtained.
Based on the criteria described above, suitable microbial hosts for the production of isobutanol include, but are not limited to, members of the genera Clostridium, Zymomonas, Escherichia, Salmonella,
Rhodococcus, Pseudomonas, Bacillus, Lactobacillus, Enterococcus, Alcaligenes, Klebsiella, Paenibacillus, Arthrobacter, Corynebacterium, Brevibacterium, Pichia, Candida, Hansenula and Saccharomyces. Preferred hosts include: Escherichia coli, Alcaligenes eutrophus, Bacillus licheniformis, Paenibacillus macerans, Rhodococcus erythropolis,
Pseudomonas putida, Lactobacillus plantarum, Enterococcus faecium, Enterococcus gallinarium, Enterococcus faecalis, Bacillus subtilis and Saccharomyces cerevisiae. Construction of Production Host
Recombinant organisms containing the necessary genes that will encode the enzymatic pathway for the conversion of a fermentable carbon substrate to isobutanol may be constructed using techniques well known in the art. Genes encoding the enzymes of one of the isobutanol biosynthetic pathways of the invention, for example, acetolactate synthase, acetohydroxy acid isomeroreductase, acetohydroxy acid dehydratase, branched-chain α-keto acid decarboxylase, and branched- chain alcohol dehydrogenase, may be isolated from various sources, as described above.
Methods of obtaining desired genes from a bacterial genome are common and well known in the art of molecular biology. For example, if the sequence of the gene is known, suitable genomic libraries may be created by restriction endonuclease digestion and may be screened with probes complementary to the desired gene sequence. Once the sequence is isolated, the DNA may be amplified using standard primer- directed amplification methods such as polymerase chain reaction (U.S. 4,683,202) to obtain amounts of DNA suitable for transformation using appropriate vectors. Tools for codon optimization for expression in a heterologous host are readily available. Some tools for codon optimization are available based on the GC content of the host organism. The GC content of some exemplary microbial hosts is given Table 3.
Table 3 GC Content of Microbial Hosts
Figure imgf000039_0001
Figure imgf000040_0001
Once the relevant pathway genes are identified and isolated they may be transformed into suitable expression hosts by means well known in the art. Vectors or cassettes useful for the transformation of a variety of host cells are common and commercially available from companies such as EPICENTRE® (Madison, Wl), Invitrogen Corp. (Carlsbad, CA),
Stratagene (La JoIIa, CA), and New England Biolabs, Inc. (Beverly, MA). Typically the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a region 5' of the gene which harbors transcriptional initiation controls and a region 3' of the DNA fragment which controls transcriptional termination. Both control regions may be derived from genes homologous to the transformed host cell, although it is to be understood that such control regions may also be derived from genes that are not native to the specific species chosen as a production host.
Initiation control regions or promoters, which are useful to drive expression of the relevant pathway coding regions in the desired host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these genetic elements is suitable for the present invention including, but not limited to, CYC1, HIS3, GAL1, GAL10, ADH 1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI, CUP1, FBA, GPD, and GPM (useful for expression in Saccharomyces); A0X1 (useful for expression in Pichia); and lac, ara, tet, trp, IPL, IPR, Tl, tac, and trc (useful for expression in Escherichia coli, Alcaligenes, and
Pseudomonas); the amy, apr, npr promoters and various phage promoters useful for expression in Bacillus subtilis, Bacillus licheniformis, and Paenibacillus macerans; nisA (useful for expression Gram-positive bacteria, Eichenbaum et al. Appl. Environ. Microbiol. 64(8):2763-2769 (1998)); and the synthetic P11 promoter (useful for expression in Lactobacillus plantarum, Rud et al., Microbiology 152:1011 -1019 (2006)).
Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary, however, it is most preferred if included.
Certain vectors are capable of replicating in a broad range of host bacteria and can be transferred by conjugation. The complete and annotated sequence of pRK404 and three related vectors-pRK437, pRK442, and pRK442(H) are available. These derivatives have proven to be valuable tools for genetic manipulation in Gram-negative bacteria
(Scott et al., Plasmid 50(1 ):74-79 (2003)). Several plasmid derivatives of broad-host-range lnc P4 plasmid RSF1010 are also available with promoters that can function in a range of Gram-negative bacteria. Plasmid pAYC36 and pAYC37, have active promoters along with multiple cloning sites to allow for the heterologous gene expression in Gram- negative bacteria.
Chromosomal gene replacement tools are also widely available. For example, a thermosensitive variant of the broad-host-range replicon pWV101 has been modified to construct a plasmid pVE6002 which can be used to effect gene replacement in a range of Gram-positive bacteria (Maguin et al., J. Bacteriol. 174(17):5633-5638 (1992)). Additionally, in vitro transposomes are available to create random mutations in a variety of genomes from commercial sources such as EPICENTRE®.
The expression of an isobutanol biosynthetic pathway in various preferred microbial hosts is described in more detail below.
Expression of an isobutanol biosynthetic pathway in E. coli
Vectors or cassettes useful for the transformation of E. coli are common and commercially available from the companies listed above. For example, the genes of an isobutanol biosynthetic pathway may be isolated from various sources, cloned into a modified pUC19 vector and transformed into E. coli NM522, as described in Examples 10 and 11. Expression of an isobutanol biosynthetic pathway in Rhodococcus ervthroDolis
A series of E. coli-Rhodococcus shuttle vectors are available for expression in R. erythropolis, including, but not limited to, pRhBR17 and pDA71 (Kostichka et al., Appl. Microbiol. Biotechnol. 62:61 -68(2003)).
Additionally, a series of promoters are available for heterologous gene expression in R. erythropolis (see for example Nakashima et al., Appl.
Environ. Microbiol. 70:5557-5568 (2004), and Tao et al., Appl. Microbiol.
Biotechnol. 2005, DOI 10.1007/s00253-005-0064). Targeted gene disruption of chromosomal genes in R. erythropolis may be created using the method described by Tao et al., supra, and Brans et al. (Appl. Environ.
Microbiol. 66: 2029-2036 (2000)).
The heterologous genes required for the production of isobutanol, as described above, may be cloned initially in pDA71 or pRhBR71 and transformed into E. coli. The vectors may then be transformed into R. erythropolis by electroporation, as described by Kostichka et al., supra.
The recombinants may be grown in synthetic medium containing glucose and the production of isobutanol can be followed using methods known in the art. Expression of an isobutanol biosvnthetic pathway in B. Subtilis
Methods for gene expression and creation of mutations in B. subtilis are also well known in the art. For example, the genes of an isobutanol biosynthetic pathway may be isolated from various sources, cloned into a modified pUC19 vector and transformed into Bacillus subtilis BE1010, as described in Example 12. Additionally, the five genes of an isobutanol biosynthetic pathway can be split into two operons for expression, as described in Example 24. The three genes of the pathway (bubB, HvD, and kivD) were integrated into the chromosome of Bacillus subtilis BE1010
(Payne and Jackson, J. Bacteriol. 173:2278-2282 (1991 )). The remaining two genes (HvC and bdhB) were cloned into an expression vector and transformed into the Bacillus strain carrying the integrated isobutanol genes Expression of an isobutanol biosynthetic pathway in B. licheniformis
Most of the plasmids and shuttle vectors that replicate in B. subtilis may be used to transform B. licheniformis by either protoplast transformation or electroporation. The genes required for the production of isobutanol may be cloned in plasmids pBE20 or pBE60 derivatives (Nagarajan et al., Gene 114:121 -126 (1992)). Methods to transform B. licheniformis are known in the art (for example see Fleming et al. Appl. Environ. Microbiol., 61 (11 ):3775-3780 (1995)). The plasmids constructed for expression in B. subtilis may be transformed into B. licheniformis to produce a recombinant microbial host that produces isobutanol.
Expression of an isobutanol biosynthetic pathway in Paenibacillus macerans
Plasmids may be constructed as described above for expression in B. subtilis and used to transform Paenibacillus macerans by protoplast transformation to produce a recombinant microbial host that produces isobutanol.
Expression of the isobutanol biosynthetic pathway in Alcaligenes (Ralstonia) eutrophus
Methods for gene expression and creation of mutations in Alcaligenes eutrophus are known in the art (see for example Taghavi et al., Appl. Environ. Microbiol., 60(10):3585-3591 (1994)). The genes for an isobutanol biosynthetic pathway may be cloned in any of the broad host range vectors described above, and electroporated to generate recombinants that produce isobutanol. The poly(hydroxybutyrate) pathway in Alcaligenes has been described in detail, a variety of genetic techniques to modify the Alcaligenes eutrophus genome is known, and those tools can be applied for engineering an isobutanol biosynthetic pathway.
Expression of an isobutanol biosynthetic pathway in Pseudomonas Dutida
Methods for gene expression in Pseudomonas putida are known in the art (see for example Ben-Bassat et al., U.S. Patent No. 6,586,229, which is incorporated herein by reference). The isobutanol pathway genes may be inserted into pPCU18 and this ligated DNA may be electroporated into electrocompetent Pseudomonas putida DOT-T1 C5aAR1 cells to generate recombinants that produce isobutanol.
Expression of an isobutanol biosvnthetic pathway in Saccharomvces cerevisiae Methods for gene expression in Saccharomyces cerevisiae are known in the art (see for example Methods in Enzymology, Volume 194, Guide to Yeast Genetics and Molecular and Cell Biology (Part A, 2004, Christine Guthrie and Gerald R. Fink (Eds.), Elsevier Academic Press, San Diego, CA). Expression of genes in yeast typically requires a promoter, followed by the gene of interest, and a transcriptional terminator. A number of yeast promoters can be used in constructing expression cassettes for genes encoding an isobutanol biosynthetic pathway, including, but not limited to constitutive promoters FBA, GPD, ADH1 , and GPM, and the inducible promoters GAL1 , GAL10, and CUP1. Suitable transcriptional terminators include, but are not limited to FBAt, GPDt, GPMt, ERGIOt, GALIt, CYC1 , and ADH1. For example, suitable promoters, transcriptional terminators, and the genes of an isobutanol biosynthetic pathway may be cloned into E. co//-yeast shuttle vectors as described in Example 21. Expression of an isobutanol biosvnthetic pathway in Lactobacillus plantarum
The Lactobacillus genus belongs to the Lactobacillales family and many plasmids and vectors used in the transformation of Bacillus subtilis and Streptococcus may be used for lactobacillus. Non-limiting examples of suitable vectors include pAMβi and derivatives thereof (Renault et al., Gene 183:175-182 (1996); and O'Sullivan et al., Gene 137:227-231 (1993)); pMBB1 and pHW800, a derivative of pMBB1 (Wyckoff et al. Appl. Environ. Microbiol. 62:1481-1486 (1996)); pMG1 , a conjugative plasmid (Tanimoto et al., J. Bacteriol. 184:5800-5804 (2002)); pNZ9520 (Kleerebezem et al., Appl. Environ. Microbiol. 63:4581 -4584 (1997)); pAM401 (Fujimoto et al., Appl. Environ. Microbiol. 67:1262-1267 (2001 )); and pAT392 (Arthur et al., Antimicrob. Agents Chemother. 38:1899-1903 (1994)). Several plasmids from Lactobacillus plantarum have also been reported (e.g., van Kranenburg R, GoNc N, Bongers R, Leer RJ, de Vos WM, Siezen RJ, Kleerebezem M. Appl. Environ. Microbiol. 2005 Mar; 71 (3): 1223-1230). For example, expression of an isobutanol biosynthetic pathway in Lactobacillus plantarum is described in Example 25. Expression of an isobutanol biosvnthetic pathway in Enterococcus faecium, Enterococcus αallinarium, and Enterococcus faecalis
The Enterococcus genus belongs to the Lactobacillales family and many plasmids and vectors used in the transformation of Lactobacillus, Bacillus subtilis, and Streptococcus may be used for Enterococcus. Non- limiting examples of suitable vectors include pAMβi and derivatives thereof (Renault et al., Gene 183:175-182 (1996); and O'Sullivan et al., Gene 137:227-231 (1993)); pMBB1 and pHW800, a derivative of pMBB1 (Wyckoff et al. Appl. Environ. Microbiol. 62:1481 -1486 (1996)); pMG1 , a conjugative plasmid (Tanimoto et al., J. Bacteriol. 184:5800-5804 (2002)); pNZ9520 (Kleerebezem et al., Appl. Environ. Microbiol. 63:4581 -4584 (1997)); pAM401 (Fujimoto et al., Appl. Environ. Microbiol. 67:1262-1267 (2001 )); and pAT392 (Arthur et al., Antimicrob. Agents Chemother. 38:1899-1903 (1994)). Expression vectors for E. faecalis using the nisA gene from Lactococcus may also be used (Eichenbaum et al., Appl. Environ. Microbiol. 64:2763-2769 (1998). Additionally, vectors for gene replacement in the E. faecium chromosome may be used (Nallaapareddy et al., Appl. Environ. Microbiol. 72:334-345 (2006)). For example, expression of an isobutanol biosynthetic pathway in Enterococcus faecalis is described in Example 26. Fermentation Media
Fermentation media in the present invention must contain suitable carbon substrates. Suitable substrates may include but are not limited to monosaccharides such as glucose and fructose, oligosaccharides such as lactose or sucrose, polysaccharides such as starch or cellulose or mixtures thereof and unpuhfied mixtures from renewable feedstocks such as cheese whey permeate, cornsteep liquor, sugar beet molasses, and barley malt. Additionally the carbon substrate may also be one-carbon substrates such as carbon dioxide, or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated. In addition to one and two carbon substrates methylotrophic organisms are also known to utilize a number of other carbon containing compounds such as methylamine, glucosamine and a variety of amino acids for metabolic activity. For example, methylotrophic yeast are known to utilize the carbon from methylamine to form trehalose or glycerol (Bellion et al., Microb. Growth C1 Compd., [Int. Symp.], 7th (1993), 415-32. Editor(s): Murrell, J. CoIMn; Kelly, Don P. Publisher: Intercept, Andover, UK). Similarly, various species of Candida will metabolize alanine or oleic acid (Suiter et al., Arch. Microbiol. 153:485-489 (1990)). Hence it is contemplated that the source of carbon utilized in the present invention may encompass a wide variety of carbon containing substrates and will only be limited by the choice of organism.
Although it is contemplated that all of the above mentioned carbon substrates and mixtures thereof are suitable in the present invention, preferred carbon substrates are glucose, fructose, and sucrose. Sucrose may be derived from renewable sugar sources such as sugar cane, sugar beets, cassava, sweet sorghum, and mixtures thereof. Glucose and dextrose may be derived from renewable grain sources through saccharification of starch based feedstocks including grains such as corn, wheat, rye, barley, oats, and mixtures thereof. In addition, fermentable sugars may be derived from renewable cellulosic or lignocellulosic biomass through processes of pretreatment and saccharification, as described, for example, in co-owned and co-pending U.S. Patent Application Publication No. 2007/0031918A1 , which is herein incorporated by reference. Biomass refers to any cellulosic or lignocellulosic material and includes materials comprising cellulose, and optionally further comprising hemicellulose, lignin, starch, oligosaccharides and/or monosaccharides. Biomass may also comprise additional components, such as protein and/or lipid. Biomass may be derived from a single source, or biomass can comprise a mixture derived from more than one source; for example, biomass may comprise a mixture of corn cobs and corn stover, or a mixture of grass and leaves. Biomass includes, but is not limited to, bioenergy crops, agricultural residues, municipal solid waste, industrial solid waste, sludge from paper manufacture, yard waste, wood and forestry waste. Examples of biomass include, but are not limited to, corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat, wheat straw, barley, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, soy, components obtained from milling of grains, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof. In addition to an appropriate carbon source, fermentation media must contain suitable minerals, salts, cofactors, buffers and other components, known to those skilled in the art, suitable for the growth of the cultures and promotion of the enzymatic pathway necessary for isobutanol production. Culture Conditions with Temperature Lowering
In the present method, the recombinant microbial production host which produces isobutanol is seeded into a fermentation medium comprising a fermentable carbon substrate to create a fermentation culture. The production host is grown in the fermentation culture at a first temperature for a first period of time. The first temperature is typically from about 25 0C to about 40 0C.
Suitable fermentation media in the present invention include common commercially prepared media such as Luria Bertani (LB) broth, Sabouraud Dextrose (SD) broth or Yeast Medium (YM) broth. Other defined or synthetic growth media may also be used, and the appropriate medium for growth of the particular microorganism will be known by one skilled in the art of microbiology or fermentation science. The use of agents known to modulate catabolite repression directly or indirectly, e.g., cyclic adenosine 2':3'-monophosphate, may also be incorporated into the fermentation medium.
Suitable pH ranges for the fermentation are between pH 5.0 to pH 9.0, where pH 6.0 to pH 8.0 is preferred as the initial condition.
Fermentations may be performed under aerobic or anaerobic conditions, where anaerobic or microaerobic conditions are preferred. The first period of time to grow the production host at the first temperature may be determined in a variety of ways. For example, during this period of growth a metabolic parameter of the fermentation culture may be monitored. The metabolic parameter that is monitored may be any parameter known in the art, including, but not limited to the optical density, pH, respiratory quotient, fermentable carbon substrate utilization, CO2 production, and isobutanol production. During this period of growth, additional fermentable carbon substrate may be added, the pH may be adjusted, oxygen may be added for aerobic cells, or other culture parameters may be adjusted to support the metabolic activity of the culture. Though nutrients and culture conditions are supportive of growth, after a period of time the metabolic activity of the fermentation culture decreases as determined by the monitored parameter described above. For example, a decrease in metabolic activity may be indicated by a decrease in one or more of the following parameters: rate of optical density change, rate of pH change, rate of change in respiratory quotient (if the host cells are aerobic), rate of fermentable carbon substrate utilization, rate of isobutanol production, rate of change in CO2 production, or rate of another metabolic parameter. The decrease in metabolic activity is related to the sensitivity of the host cells to the production of isobutanol and/or the presence of isobutanol in the culture. When decreased metabolic activity is detected, the temperature of the fermentation culture is lowered to reduce the sensitivity of the host cells to isobutanol and thereby allow further production of isobutanol. In one embodiment, the lowering of the temperature coincides with a change in the metabolic parameter that is monitored.
In one embodiment, the change in metabolic activity is a decrease in the rate of isobutanol production. Isobutanol production may be monitored by analyzing the amount of isobutanol present in the fermentation culture medium as a function of time using methods well known in the art, such as using high performance liquid chromatography (HPLC) or gas chromatography (GC), which are described in the Examples herein. GC is preferred due to the short assay time. Alternatively, the lowering of the temperature of the fermentation culture may occur at a predetermined time. The first period of time may be predetermined by establishing a correlation between a metabolic parameter of the fermentation culture and time in a series of test fermentations runs. A correlation between a metabolic parameter, as described above, and time of culture growth may be established for any isobutanol producing host by one skilled in the art. The specific correlation may vary depending on conditions used including, but not limited to, carbon substrate, fermentation conditions, and the specific recombinant isobutanol producing microbial production host. The correlation is most suitably made between isobutanol production or specific glucose consumption rate and time of culture growth. Once the predetermined time has been established from the correlation, the temperature of the fermentation culture in subsequent fermentation runs is lowered at the predetermined time. For example, if it is determined by monitoring a metabolic parameter in the test fermentation runs that the rate of production of isobutanol decreases after 12 hours, the temperature in subsequent fermentations runs is lowered after 12 hours without the need to monitor isobutanol production in the subsequent runs. After the first period of time, the temperature of the fermentation culture is lowered to a second temperature. Typically, the second temperature is about 3 0C to about 25 0C lower than the first temperature. Reduction in temperature to enhance tolerance of the host cells to isobutanol is balanced with maintaining the temperature at a level where the cells continue to be metabolically active for isobutanol production. For example, a fermentation culture that has been grown at about 35 0C may be reduced in temperature to about 28 0C; or a culture grown at about 30 0C may be reduced in temperature to about 25 0C. The change in temperature may be done gradually over time or may be made as a step change. The production host is incubated at the second temperature for a second period of time, so that isobutanol production continues. The second period of time may be determined in the same manner as the first period of time described above, e.g., by monitoring a metabolic parameter or by using a predetermined time. Additionally, the temperature lowering and incubation steps may be repeated one or more times to more finely balance metabolic activity for isobutanol production and isobutanol sensitivity. For example, a culture that has been grown at about 35 0C may be reduced in temperature to about 32 0C, followed by an incubation period. During this period a metabolic parameter of the fermentation culture may be monitored as described above, or a predetermined time may be used. It is particularly suitable to monitor the production of isobutanol during this incubation period. When monitoring indicates a decrease in metabolic activity or at a predetermined time, the temperature may be reduced a second time. For example, the temperature may be reduced from about 32 0C to about 28 0C. The temperature lowering and incubation steps may be repeated a third time where the temperature is reduced, for example, to about 20 0C. The production host is incubated at the lowered temperature so that isobutanol production continues. The steps may be repeated further as necessary to obtain the desired isobutanol titer. Industrial Batch and Continuous Fermentations
The present process employs a batch method of fermentation. A classical batch fermentation is a closed system where the composition of the medium is set at the beginning of the fermentation and not subject to artificial alterations during the fermentation. Thus, at the beginning of the fermentation the medium is inoculated with the desired organism or organisms, and fermentation is permitted to occur without adding anything to the system. Typically, however, a "batch" fermentation is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems the metabolite and biomass compositions of the system change constantly up to the time the fermentation is stopped. Within batch cultures cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in log phase generally are responsible for the bulk of production of end product or intermediate. A variation on the standard batch system is the Fed-Batch system. Fed-Batch fermentation processes are also suitable in the present invention and comprise a typical batch system with the exception that the substrate is added in increments as the fermentation progresses. Fed-Batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO2. Batch and Fed-Batch fermentations are common and well known in the art and examples may be found in Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, MA., or Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36:227, (1992), herein incorporated by reference.
Although the present invention is performed in batch mode it is contemplated that the method would be adaptable to continuous fermentation methods. Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth.
Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate. In other systems a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to the medium being drawn off must be balanced against the cell growth rate in the fermentation. Methods of modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock, supra.
It is contemplated that the present invention may be practiced using either batch, fed-batch or continuous processes and that any known mode of fermentation would be suitable. Additionally, it is contemplated that cells may be immobilized on a substrate as whole cell catalysts and subjected to fermentation conditions for isobutanol production. Methods for lsobutanol Isolation from the Fermentation Medium
The bioproduced isobutanol may be isolated from the fermentation medium using methods known in the art. For example, solids may be removed from the fermentation medium by centrifugation, filtration, decantation, or the like. Then, the isobutanol may be isolated from the fermentation medium, which has been treated to remove solids as described above, using methods such as distillation, liquid-liquid extraction, or membrane-based separation. Because isobutanol forms a low boiling point, azeotropic mixture with water, distillation can only be used to separate the mixture up to its azeotropic composition. Distillation may be used in combination with another separation method to obtain separation around the azeotrope. Methods that may be used in combination with distillation to isolate and purify isobutanol include, but are not limited to, decantation, liquid-liquid extraction, adsorption, and membrane-based techniques. Additionally, isobutanol may be isolated using azeotropic distillation using an entrainer (see for example Doherty and Malone, Conceptual Design of Distillation Systems, McGraw Hill, New York, 2001 ).
The isobutanol-water mixture forms a heterogeneous azeotrope so that distillation may be used in combination with decantation to isolate and purify the isobutanol. In this method, the isobutanol containing fermentation broth is distilled to near the azeotropic composition. Then, the azeotropic mixture is condensed, and the isobutanol is separated from the fermentation medium by decantation. The decanted aqueous phase may be returned to the first distillation column as reflux. The isobutanol- rich decanted organic phase may be further purified by distillation in a second distillation column. The isobutanol may also be isolated from the fermentation medium using liquid-liquid extraction in combination with distillation. In this method, the isobutanol is extracted from the fermentation broth using liquid-liquid extraction with a suitable solvent. The isobutanol-containing organic phase is then distilled to separate the isobutanol from the solvent.
Distillation in combination with adsorption may also be used to isolate isobutanol from the fermentation medium. In this method, the fermentation broth containing the isobutanol is distilled to near the azeotropic composition and then the remaining water is removed by use of an adsorbent, such as molecular sieves (Aden et al. Lignocellulosic
Biomass to Ethanol Process Design and Economics Utilizing Co-Current Dilute Acid Prehydrolysis and Enzymatic Hydrolysis for Corn Stover, Report NREL/TP-510-32438, National Renewable Energy Laboratory, June 2002). Additionally, distillation in combination with pervaporation may be used to isolate and purify the isobutanol from the fermentation medium. In this method, the fermentation broth containing the isobutanol is distilled to near the azeotropic composition, and then the remaining water is removed by pervaporation through a hydrophilic membrane (Guo et al., J. Membr. Sci. 245, 199-210 (2004)).
EXAMPLES
The present invention is further defined in the following Examples. It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various uses and conditions. General Methods
Standard recombinant DNA and molecular cloning techniques used in the Examples are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY (1989) (Maniatis) and by T. J. Silhavy, M. L. Bennan, and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1984) and by Ausubel, F. M. et ai, Current Protocols in Molecular Biology, pub. by Greene Publishing Assoc, and Wiley-lnterscience (1987).
Materials and methods suitable for the maintenance and growth of bacterial cultures are well known in the art. Techniques suitable for use in the following Examples may be found as set out in Manual of Methods for General Bacteriology (Phillipp Gerhardt, R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester, Willis A. Wood, Noel R. Krieg and G. Briggs Phillips, eds), American Society for Microbiology, Washington, DC. (1994)) or by Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition, Sinauer Associates, Inc., Sunderland, MA (1989). All reagents, restriction enzymes and materials used for the growth and maintenance of bacterial cells were obtained from Aldrich Chemicals (Milwaukee, Wl), BD Diagnostic Systems (Sparks, MD), Life Technologies (Rockville, MD), or Sigma Chemical Company (St. Louis, MO) unless otherwise specified.
Microbial strains were obtained from The American Type Culture Collection (ATCC), Manassas, VA, unless otherwise noted.
The oligonucleotide primers to use in the following Examples are given in Table 4. All the oligonucleotide primers are synthesized by Sigma-Genosys (Woodlands, TX).
Table 4 Oligonucleotide Cloning, Screening, and Sequencing Primers
Figure imgf000054_0001
Figure imgf000055_0001
Figure imgf000056_0001
Figure imgf000057_0001
Figure imgf000058_0001
Figure imgf000059_0001
Figure imgf000060_0001
Methods for Determining lsobutanol Concentration in Culture Media
The concentration of isobutanol in the culture media can be determined by a number of methods known in the art. For example, a specific high performance liquid chromatography (HPLC) method utilized a Shodex SH-1011 column with a Shodex SH-G guard column, both purchased from Waters Corporation (Milford, MA), with refractive index (Rl) detection. Chromatographic separation was achieved using 0.01 M H2SO4 as the mobile phase with a flow rate of 0.5 mL/min and a column temperature of 50 0C. Isobutanol had a retention time of 46.6 min under the conditions used. Alternatively, gas chromatography (GC) methods are available. For example, a specific GC method utilized an HP-INNOWax column (30 m x 0.53 mm id,1 μm film thickness, Agilent Technologies, Wilmington, DE), with a flame ionization detector (FID). The carrier gas was helium at a flow rate of 4.5 mL/min, measured at 150 0C with constant head pressure; injector split was 1 :25 at 200 0C; oven temperature was 45 0C for 1 min, 45 to 220 0C at 10 °C/min, and 220 0C for 5 min; and FID detection was employed at 240 0C with 26 mL/min helium makeup gas. The retention time of isobutanol was 4.5 min. The meaning of abbreviations is as follows: "s" means second(s), "min" means minute(s), "h" means hour(s), "psi" means pounds per square inch, "nm" means nanometers, "d" means day(s), "μl_" means microliter(s), "mL" means milliliter(s), "L" means liter(s), "mm" means millimeter(s), "nm" means nanometers, "mM" means millimolar, "μM" means micromolar, "M" means molar, "mmol" means millimole(s), "μmol" means micromole(s)", "g" means gram(s), "μg" means microgram(s) and "ng" means nanogram(s), "PCR" means polymerase chain reaction, "OD" means optical density, "OD6oo" means the optical density measured at a wavelength of 600 nm, "kDa" means kilodaltons, "g" means the gravitation constant, "bp" means base pair(s), "kbp" means kilobase pair(s), "% w/v" means weight/volume percent, % v/v" means volume/volume percent, "IPTG" means isopropyl-β- D-thiogalactopyranoiside, "RBS" means ribosome binding site, "nt" means not tested, "HPLC" means high performance liquid chromatography, and "GC" means gas chromatography. The term "molar selectivity" is the number of moles of product produced per mole of sugar substrate consumed and is reported as a percent.
EXAMPLE 1 Increased tolerance of Lactobacillus plantarum PN0512 to 1 -butanol, iso- butanol and 2-butanol at decreased growth temperatures
Tolerance levels of bacterial strain Lactobacillus plantarum PN0512 (ATCC # PTA-7727) were determined at 25 0C, 30 0C and 37 0C as follows. The strain was cultured in S30L medium (i.e., 10 mM ammonium sulfate, 5 mM potassium phosphate buffer, pH 7.0, 50 mM MOPS, pH 7.0, 2 mM MgCI2, 0.7 mM CaCI2, 50 μM MnCI2, 1 μM FeCI3, 1 μM ZnCI2, 1.72 μM CuCI2, 2.53 μM CoCI2, 2.42 μM Na2MoO4, 2 μM thiamine hydrochloride, 10 mM glucose, and 0.2% yeast extract). An overnight culture in the absence of any test compound was started in 15 mL of the S30L medium in a 150 mL flask, with incubation at 37 0C in a shaking water bath. The next morning, the overnight culture was diluted into three
500 mL flasks containing 150 mL of fresh medium to an initial OD600 of about 0.08. Each flask was incubated in a shaking water bath, one each at 25 0C, 30 0C and 37 0C. Each large culture was allowed to acclimate at the test temperature for at least 0.5 h. After the acclimation period, each large culture was split into flasks in the absence (control) and in the presence of various amounts of 1 -butanol, isobutanol or 2-butanol, as listed in Tables 5, 6, and 7, respectively. Growth was followed by measuring OD600 for six hours after addition of the compounds. The results are summarized in Tables 5, 6, and 7 below.
Table 5. Growth of L. plantarum PN0512 in the presence of 1 -butanol at different temperatures
Figure imgf000062_0001
Table 6. Growth of L. plantarum PN0512 in the presence of isobutanol at different temperatures
Figure imgf000063_0001
Table 7. Growth of L. Dlantarum PN0512 in the presence of 2-butanol at different temperatures
Concentration 2- 37 0C 30 ' O 25 0C butanol (% w/v)
0 0 + + +
Figure imgf000064_0001
"+" = growth observed as an increase in OD600. -" = no growth observed, i.e. no change in OD600.
All three butanols showed a similar effect of temperature on growth inhibition of L. plantarum PN0512. The concentration that resulted in full growth inhibition was greater at 25 0C than at 37 0C. In the case of 1- butanol, growth was observed at 37 0C in 2.3% 1 -butanol, but not 2.4%. However, at 30 0C growth was observed in 2.7%, but not 2.9%, and at 25 0C growth was observed even in 3.1 % 1-butanol. Thus, the concentration of 1 -butanol that completely inhibited growth increased as growth temperature decreased. Likewise, in the case of isobutanol, growth was observed in 3.5% at 25 0C while growth was observed in 3.1 % at 30 0C and 37 0C, but not in 3.3% or 3.4%. Similarly, in the case of 2-butanol growth was observed at 370C in 4.3%, but not in 4.5%; at 30 0C in 4.7%, but not in 4.9%; and at 25 0C in 5.2 %. Thus the tolerance of L. plantarum PN0512 to butanols increased with decreased growth temperature. EXAMPLE 2 Increased tolerance of Escherichia coli to 1 -butanol at decreased exposure temperature
The effect of growth and exposure temperature on survival of Escherichia coli in the presence of 1-butanol was tested using stationary phase cultures in a rich medium and log phase cultures in a defined medium. For the stationary phase studies, E. coli strain MG1655 (ATCC # 700926) was grown overnight in LB medium (Teknova, Half Moon Bay, CA) with shaking at 250 rpm at 42 0C, 29 0C or 28 0C. Survival of 1 - butanol shock was tested at exposure temperatures of 0 0C, 28 0C or 42 0C. The 1 -butanol exposure at 28 0C or 42 0C was started immediately after removing the overnight cultures from the growth incubators. The 1 - butanol exposure at 0 0C was done after allowing the overnight cultures to cool on ice for about 15 min. A series of solutions of 1 -butanol at different concentrations in LB medium was made and 90 μL aliquots were put in microfuge tubes. To these were added 10 μL of the overnight cultures and the tubes were immediately placed in shaking incubators at 42 0C or 28 0C or left on ice for 30 min. To stop the effect of 1 -butanol on the cultures, a 10~2 dilution was done by placing 2 μL of the treated culture into 198 μL of LB medium in wells of a microplate. Then, 5 μL of the undiluted treated cultures were spotted on LB agar plates. Subsequent 10-fold serial dilutions of 10~3, 10~4, 10~5 and 10~6 of the exposed cultures were done by serial pipetting of 20 μL, starting with the 10~2 dilution cultures, into 180 μL of LB medium in the microplate, using a multi-channel pipette. Prior to each transfer, the cultures were mixed by pipetting up and down six times. Each dilution (5 μL) was spotted onto an LB plate using a multi-channel pipette and allowed to soak into the plate. The plates were inverted and incubated overnight at 37 0C. The number of colonies for each dilution was counted and the % growth inhibition was calculated by comparison with a control culture that had not been exposed to 1 -butanol. Survival of 0% was recorded when no colonies in the spots of the undiluted or any of the serial dilutions were observed. The results are shown in Table 8. Table 8. Survival of stationary phase E. coli in 1 -butanol at 42 0C, 28 0C, Or O 0C
Figure imgf000066_0001
A similar study was done with log-phase cultures of E. coli grown in a defined medium. E. coli strain MG1655 was allowed to grow overnight in MOPS 0.2% glucose medium (Teknova, Half Moon Bay, CA) at 42 0C or 28 0C. The following day, the cultures were diluted into fresh medium and allowed to grow at the same temperature until in the log phase of growth.
The OD600 was 0.74 for the 28 0C culture and was 0.72 for the 42 0C culture. Both of these log phase cultures were exposed to 1 -butanol at 42 0C, 28 0C and 0 0C as follows. A series of solutions of 1 -butanol at different concentrations in MOPS 0.2% glucose medium was made and 90 μl_ aliquots were put in microfuge tubes. To these were added 10 μL of the log phase cultures and the tubes were immediately placed in shaking incubators at 42 0C or 28 0C or left on ice for 30 min. To stop the effect of 1 -butanol on the cultures, a 102 dilution was done by placing 2 μL of the treated culture into 198 μL of LB medium in wells of a microplate. Then 5 μl_ of the undiluted treated cultures were spotted on LB agar plates. Subsequent 10-fold serial dilutions of 10~3, 10~4, 10~5 and 10~6 of the exposed cultures were done by serial pipetting of 20 μl_, starting with the 10~2 dilution cultures, into 180 μl_ of LB medium in the microplate, using a multi-channel pipette. Prior to each transfer, the cultures were mixed by pipetting up and down six times. Each dilution (5 μL) was spotted onto an LB plate using a multi-channel pipette and allowed to soak into the plate. The plates were inverted and incubated overnight at 37 0C. The number of colonies for each dilution was counted and the % growth inhibition was calculated by comparison with a control culture that had not been exposed to 1 -butanol. Survival of 0% was recorded when no colonies in the spots of the undiluted or any of the serial dilutions were observed. The results are shown in Table 9.
Table 9. Survival of log-phase E. coli in 1-butanol at 42 0C, 28 0C, or 0 0C
Figure imgf000067_0001
For both the stationary phase and log-phase cultures of E. coli MG1655, the growth temperature had very little, if any, effect on the survival of a 1-butanol shock. However, the exposure temperature had a major effect on the survival of E. coli to 1 -butanol shock. As can be seen from the data in Tables 8 and 9, the tolerance of E. coli MG1655 to 1- butanol increased with decreasing exposure temperature.
EXAMPLE 3
Increased tolerance of Escherichia coli to 2-butanone at decreased exposure temperature The effect of exposure temperature on survival of Escherichia coli in the presence of 2-butanone (also referred to herein as methyl ethyl ketone or MEK) was tested as follows. E. coli strain BW25113 (The Coli Genetic Stock Center (CGSC), Yale University; # 7636) was grown overnight in LB medium (Teknova, Half Moon Bay, CA) with shaking at 250 rpm at 37 0C. Survival of MEK shock was tested at exposure temperatures of 28 0C or 37 0C. A series of solutions of MEK at different concentrations in LB medium was made and 90 μL aliquots were put in microfuge tubes. To these were added 10 μL of the overnight culture and the tubes were immediately placed in shaking incubators at 37 0C or 28 0C for 30 min. To stop the effect of MEK on the cultures, a 10~2 dilution was done by placing 2 μL of the MEK treated culture into 198 μL of LB medium in wells of a microplate. Then 5 μL of the undiluted treated cultures were spotted on LB agar plates. Subsequent 10-fold serial dilutions of 10~3, 10~4, 10~5 and 10~6 of the exposed cultures were done by serial pipetting of 20 μL, starting with the 10~2 dilution cultures, into 180 μL of LB medium in the microplate, using a multi-channel pipette. Prior to each transfer, the cultures were mixed by pipetting up and down six times. Each dilution (5 μL) was spotted onto LB plates using a multi-channel pipette and allowed to soak into the plate. The plates were inverted and incubated overnight at 37 0C. The number of colonies for each dilution was counted and the % growth inhibition was calculated by comparison with a control culture that had not been exposed to MEK. Survival of 0% was recorded when no colonies in the spots of the undiluted or any of the serial dilutions were observed. The results, given as the average of duplicate experiments, are shown in Table 10.
Table 10. Survival of E. coli in MEK at 37 0C and 28 0C
Figure imgf000069_0001
Reducing the exposure temperature from 37 0C to 28 0C dramatically improved survival of E. coli to MEK treatment. At 37 0C there was full survival at 4% w/v and no survival at 6% w/v, while at 28 0C there was full survival at 6% w/v. Thus, the tolerance of E. coli to MEK increased with decreasing exposure temperature.
EXAMPLE 4 Increased tolerance of E. coli and L plantarum PN0512 to 1 -Butanol at decreased exposure temperature This Example demonstrates that the toxic effects of 1 -butanol and
2-butanol on various microbial cells was reduced at lower temperatures. This was demonstrated by incubating E. coli (strain MG1655; ATCC # 700926), and L. plantarum (strain PN0512; ATCC # PTA-7727) with either 1 -butanol or 2-butanol at different temperatures and then determining the fraction of the cells that survived the treatment at the different temperatures.
Using overnight cultures or cells from plates, 30 ml_ cultures of the microorganisms to be tested were started in the following culture media:
E. coli - Miller's LB medium (Teknova, Half Moon Bay, CA): L. plantarum PN0512 - Lactobacilli MRS Broth (BD Diagnostic
Systems, Sparks, MD). The E. coli and L. plantarum cultures were grown at 37 0C aerobically with shaking until the cultures were in log phase and the OD600 was between 0.6 and 0.8. A 50 μl_ aliquot of each culture was removed for a time zero sample. The remainder of the cultures was divided into six 5 ml_ portions and placed in six small incubation flasks or tubes. Different amounts of 1 - butanol or 2-butanol were added to the six flasks to bring the concentration to predetermined values, as listed in the tables below. The flasks or tubes were incubated at a desired temperature, aerobically without shaking for 1 h. After the incubation with one of the butanols, 2 μL from each of the flasks (and in addition 2 μl_ of the time zero sample of the culture before exposure to one of the butanols) were pipetted into the "head" wells of a 96 well (8 X 12) microtiter plate, each containing 198 μL of LB medium to give a 10"2 dilution of the culture. Subsequently, 10"3, 10~4, 10~5, and 10~6 serial dilutions of the cultures were prepared as follows. The 10~3 dilution was prepared by pipetting 20 μl_ of the sample from the head well into the 180 μl_ LB medium in the next well using a multi- channel pipette. This procedure was repeated 3 more times on successive wells to prepare the 10~4, 10~5, and 10~6 dilutions. After each liquid transfer, the solution in the well was mixed by pipetting it up and down 10 times with the multi-channel pipetor. A 5 μL aliquot of each dilution was spotted onto an LB plate using a multi-channel pipette starting with the 10~6 dilution, then the 10~5, and so on working from more to less dilute without a change of tips. The spots were allowed to soak into the agar by leaving the lid of the plate slightly open for 15 to 30 min in a sterile transfer hood. The plates were covered, inverted, and incubated overnight at 37 0C. The following day, the number of colonies in the spots were counted from the different dilutions. The number of living cells/mL in each of the original culture solutions from which the 2 μL was withdrawn was calculated and compared to the number of cells in the control untreated culture to determine the % of the cells surviving.
The results of experiments in which E. coli cells were treated with 1 - butanol at temperatures of 0, 30, and 37 0C are shown Table 11. Table 11. Percentage of E. coli cells surviving in 1 -butanol at 0, 30 and 37 0C
Figure imgf000071_0001
The concentration at which 1 -butanol kills E. coli cells was affected by the treatment temperature. At 0 0C, concentrations of 1-butanol as high as 4.5% v/v had no toxic effect on E. coli cells during a one hour treatment. At 30 0C, E. coli cells were killed when treated with 3% v/v 1 - butanol for one hour. At 37 0C, E. coli cells were killed when treated with 2% v/v 1 -butanol for one hour.
The results of experiments in which L. plantarum PN0512 cells were treated with 1-butanol at temperatures of 0, 23, and 37 0C for one hour are shown Table 12.
Table 12. Percentage of L plantarum PN0512 cells surviving in 1 -butanol at 0, 23 and 37 0C
1 -butanol % Survival at O 0C % Survival at 23 0C % Survival at 37 0C % v/v
0 100 100 100
1 nt nt 80
1.5 nt nt 58
Figure imgf000072_0001
The concentration at which 1 -butanol kills L. plantarum PN0512 cells was affected by the treatment temperature. At 0 0C, concentrations of 1 -butanol as high as 4.5% v/v had no toxic effect on L. plantarum PN0512 cells during a one hour treatment. At 23 0C, L. plantarum PN0512 cells were killed when treated with 3.5% v/v 1 -butanol for one hour. At 37 0C, L. plantarum PN0512 cells were killed when treated with 2.5 % v/v 1 -butanol for one hour.
EXAMPLE 5 Cloning and Expression of Acetolactate Synthase
The purpose of this Example was to clone the budB gene from Klebsiella pneumoniae and express it in E. coli BL21 -AI. The budB gene was amplified from Klebsiella pneumoniae strain ATCC 25955 genomic DNA using PCR, resulting in a 1.8 kbp product.
Genomic DNA was prepared using the Gentra Puregene kit (Gentra Systems, Inc., Minneapolis, MN; catalog number D-5000A). The budB gene was amplified from Klebsiella pneumoniae genomic DNA by PCR using primers N80 and N81 (see Table 2), given as SEQ ID NOs:11 and 12, respectively. Other PCR amplification reagents were supplied in manufacturers' kits, for example, Finnzymes Phusion™ High-Fidelity PCR Master Mix (New England Biolabs Inc., Beverly, MA; catalog no. F-531 ) and used according to the manufacturer's protocol. Amplification was carried out in a DNA Thermocycler GeneAmp 9700 (PE Applied Biosystems, Foster city, CA).
For expression studies the Gateway cloning technology (Invitrogen Corp., Carlsbad, CA) was used. The entry vector pENTRSDD-TOPO allowed directional cloning and provided a Shine-Dalgarno sequence for the gene of interest. The destination vector pDEST14 used a T7 promoter for expression of the gene with no tag. The forward primer incorporated four bases (CACC) immediately adjacent to the translational start codon to allow directional cloning into pENTRSDD-TOPO (Invitrogen) to generate the plasmid pENTRSDD-TOPObudB. The pENTR construct was transformed into E. coli Top10 (Invitrogen) cells and plated according to manufacturer's recommendations. Transformants were grown overnight and plasmid DNA was prepared using the QIAprep Spin Miniprep kit (Qiagen, Valencia, CA; catalog no. 27106) according to manufacturer's recommendations. Clones were sequenced to confirm that the genes inserted in the correct orientation and to confirm the sequence. The nucleotide sequence of the open reading frame (ORF) for this gene and the predicted amino acid sequence of the enzyme are given as SEQ ID NO:1 and SEQ ID NO:2, respectively.
To create an expression clone, the budB gene was transferred to the pDEST 14 vector by recombination to generate pDEST14budB. The pDEST14budB vector was transformed into E. coli BL21 -AI cells (Invitrogen). Transformants were inoculated into Luria Bertani (LB) medium supplemented with 50 μg/mL of ampicillin and grown overnight. An aliquot of the overnight culture was used to inoculate 50 ml_ of LB supplemented with 50 μg/mL of ampicillin. The culture was incubated at 37 0C with shaking until the OD6oo reached 0.6-0.8. The culture was split into two 25-mL cultures and arabinose was added to one of the flasks to a final concentration of 0.2% w/v. The negative control flask was not induced with arabinose. The flasks were incubated for 4 h at 37 0C with shaking. Cells were harvested by centhfugation and the cell pellets were resuspended in 50 mM MOPS, pH 7.0 buffer. The cells were disrupted either by sonication or by passage through a French Pressure Cell. The whole cell lysate was centrifuged yielding the supernatant or cell free extract and the pellet or the insoluble fraction. An aliquot of each fraction (whole cell lysate, cell free extract and insoluble fraction) was resuspended in SDS (MES) loading buffer (Invitrogen), heated to 85 0C for 10 min and subjected to SDS-PAGE analysis (NuPAGE 4-12% Bis-Tris Gel, catalog no. NP0322Box, Invitrogen). A protein of the expected molecular weight of about 60 kDa, as deduced from the nucleic acid sequence, was present in the induced culture but not in the uninduced control. Acetolactate synthase activity in the cell free extracts is measured using the method described by Bauerle et al. (Biochim. Biophys. Acta 92(1 ):142-149 (1964)).
Example 6 (Prophetic) Cloning and Expression of Acetohvdroxy Acid Reductoisomerase The purpose of this prophetic Example is to describe how to clone the HvC gene from E. coli K12 and express it in E. coli BL21 -AI. The HvC gene is amplified from E. coli genomic DNA using PCR.
The HvC gene is cloned and expressed in the same manner as the budB gene described in Example 5. Genomic DNA from E. coli is prepared using the Gentra Puregene kit (Gentra Systems, Inc.,
Minneapolis, MN; catalog number D-5000A). The HvC gene is amplified by PCR using primers N100 and N101 (see Table 2), given as SEQ ID NOs: 13 and 14, respectively, creating a 1.5 kbp product. The forward primer incorporates four bases (CCAC) immediately adjacent to the translational start codon to allow directional cloning into pENTR/SD/D- TOPO (Invitrogen) to generate the plasmid pENTRSDD-TOPOilvC. Clones are sequenced to confirm that the genes are inserted in the correct orientation and to confirm the sequence. The nucleotide sequence of the open reading frame (ORF) for this gene and the predicted amino acid sequence of the enzyme are given as SEQ ID NO:3 and SEQ ID NO:4, respectively.
To create an expression clone, the HvC gene is transferred to the pDEST 14 (Invitrogen) vector by recombination to generate pDEST14ilvC. The pDEST14ilvC vector is transformed into E. coli BL21 -AI cells and expression from the T7 promoter is induced by addition of arabinose. A protein of the expected molecular weight of about 54 kDa, as deduced from the nucleic acid sequence, is present in the induced culture, but not in the uninduced control. Acetohydroxy acid reductoisomerase activity in the cell free extracts is measured using the method described by Arfin and Umbarger (J. Biol. Chem. 244(5):1118-1127 (1969)).
Example 7 (Prophetic) Cloning and Expression of Acetohvdroxy Acid Dehydratase
The purpose of this prophetic Example is to describe how to clone the HvD gene from E. coli K12 and express it in E. coli BL21 -AI. The HvD gene is amplified from E. coli genomic DNA using PCR.
The HvD gene is cloned and expressed in the same manner as the budB gene described in Example 5. Genomic DNA from E. coli is prepared using the Gentra Puregene kit (Gentra Systems, Inc., Minneapolis, MN; catalog number D-5000A). The HvD gene is amplified by PCR using primers N102 and N103 (see Table 2), given as SEQ ID NOs: 15 and 16, respectively, creating a 1.9 kbp product. The forward primer incorporates four bases (CCAC) immediately adjacent to the translational start codon to allow directional cloning into pENTR/SD/D- TOPO (Invitrogen) to generate the plasmid pENTRSDD-TOPOilvD. Clones are submitted for sequencing to confirm that the genes are inserted in the correct orientation and to confirm the sequence. The nucleotide sequence of the open reading frame (ORF) for this gene and the predicted amino acid sequence of the enzyme are given as SEQ ID NO:5 and SEQ ID NO:6, respectively.
To create an expression clone, the HvD gene is transferred to the pDEST 14 (Invitrogen) vector by recombination to generate pDEST14ilvD. The pDEST14ilvD vector is transformed into E. coli BL21 -AI cells and expression from the T7 promoter is induced by addition of arabinose. A protein of the expected molecular weight of about 66 kDa, as deduced from the nucleic acid sequence, is present in the induced culture, but not in the uninduced control. Acetohydroxy acid dehydratase activity in the cell free extracts is measured using the method described by Flint et al. (J. Biol. Chem. 268(20):14732-14742 (1993)). Example 8 (Prophetic)
Cloning and Expression of Branched-Chain Keto Acid Decarboxylase The purpose of this prophetic example is to describe how to clone the kivD gene from Lactococcus lactis and express it in E. coli BL21-AI. A DNA sequence encoding the branched-chain keto acid decarboxylase (kivD) from L. lactis is obtained from GenScript (Piscataway, NJ). The sequence obtained is codon-optimized for expression in both E. coli and B. subtilis and is cloned into pUC57, to form pUC57-kivD. The codon-optimized nucleotide sequence of the open reading frame (ORF) for this gene and the predicted amino acid sequence of the enzyme are given as SEQ ID NO:7 and SEQ ID NO:8, respectively. To create an expression clone Ndel and BamHI restriction sites are utilized to clone the 1.7 kbp kivD fragment from pUC57-kivD into vector pET-3a (Novagen, Madison, Wl). This creates the expression clone pET- 3a-kivD. The pET-3a-kivD vector is transformed into E. coli BL21-AI cells and expression from the T7 promoter is induced by addition of arabinose. A protein of the expected molecular weight of about 61 kDa, as deduced from the nucleic acid sequence, is present in the induced culture, but not in the uninduced control. Branched-chain keto acid decarboxylase activity in the cell free extracts is measured using the method described by Smit et al. {Appl. Microbiol. Biotech nol. 64:396-402 (2003)).
Example 9 (Prophetic)
Cloning and Expression of Branched-Chain Alcohol Dehydrogenase The purpose of this prophetic Example is to describe how to clone the yqhD gene from E. coli K12 and express it in E. coli BL21 -AI. The yqhD gene is amplified from E. coli genomic DNA using PCR.
The yqhD gene is cloned and expressed in the same manner as the budB gene described in Example 5. Genomic DNA from E. coli is prepared using the Gentra Puregene kit (Gentra Systems, Inc.,
Minneapolis, MN; catalog number D-5000A). The yqhD gene is amplified by PCR using primers N104 and N105 (see Table 2), given as SEQ ID NOs: 17 and 18, respectively, creating a 1.2 kbp product. The forward primer incorporates four bases (CCAC) immediately adjacent to the translational start codon to allow directional cloning into pENTR/SD/D- TOPO (Invitrogen) to generate the plasmid pENTRSDD-TOPOyqhD. Clones are submitted for sequencing to confirm that the genes are inserted in the correct orientation and to confirm the sequence. The nucleotide sequence of the open reading frame (ORF) for this gene and the predicted amino acid sequence of the enzyme are given as SEQ ID NO 9 and SEQ ID NO:10, respectively.
To create an expression clone, the yqhD gene is transferred to the pDEST 14 (Invitrogen) vector by recombination to generate pDEST14yqhD. The pDEST14ilvD vector is transformed into E. coli BL21 - Al cells and expression from the T7 promoter is induced by addition of arabinose. A protein of the expected molecular weight of about 42 kDa, as deduced from the nucleic acid sequence, is present in the induced culture, but not in the uninduced control. Branched-chain alcohol dehydrogenase activity in the cell free extracts is measured using the method described by Sulzenbacher et al. (J. MoI. Biol. 342(2):489-502 (2004)).
Example 10 (Prophetic) Construction of a Transformation Vector for the Genes in an lsobutanol Biosvnthetic Pathway
The purpose of this prophetic Example is to describe how to construct a transformation vector comprising the genes encoding the five steps in an isobutanol biosynthetic pathway. All genes are placed in a single operon under the control of a single promoter. The individual genes are amplified by PCR with primers that incorporate restriction sites for later cloning and the forward primers contain an optimized E. coli hbosome binding site (AAAGGAGG). PCR products are TOPO cloned into the pCR 4Blunt-TOPO vector and transformed into E. coli Top10 cells (Invitrogen). Plasmid DNA is prepared from the TOPO clones and the sequence of the genes is verified. Restriction enzymes and T4 DNA ligase (New England Biolabs, Beverly, MA) are used according to manufacturer's recommendations. For cloning experiments, restriction fragments are gel- purified using QIAquick Gel Extraction kit (Qiagen). After confirmation of the sequence, the genes are subcloned into a modified pUC19 vector as a cloning platform. The pUC19 vector is modified by Hindlll/Sapl digestion, creating pUC19dHS. The digest removes the lac promoter adjacent to the MCS (multiple cloning site), preventing transcription of the operons in the vector. The budB gene is amplified from K. pneumoniae ATCC 25955 genomic DNA by PCR using primer pair N110 and N111 (see Table 2), given as SEQ ID NOs:19 and 20, respectively, creating a 1.8 kbp product. The forward primer incorporates Sphl and AfIII restriction sites and a hbosome binding site (RBS). The reverse primer incorporates Pad and Nsil restriction sites. The PCR product is cloned into pCR4 Blunt-TOPO creating pCR4 Blunt-TOPO-budB. Plasmid DNA is prepared from the TOPO clones and the sequence of the gene is verified.
The HvC gene is amplified from E. coli K12 genomic DNA by PCR using primer pair N112 and N113 (see Table 2) given as SEQ ID NOs:21 and 22, respectively, creating a 1.5 kbp product. The forward primer incorporates Sail and Nhel restriction sites and a RBS. The reverse primer incorporates a Xbal restriction site. The PCR product is cloned into pCR4 Blunt-TOPO creating pCR4 Blunt-TOPO-ilvC. Plasmid DNA is prepared from the TOPO clones and the sequence of the gene is verified. The HvD gene is amplified from E. coli K12 genomic DNA by PCR using primer pair N114 and N115 (see Table 2) given as SEQ ID NOs:23 and 24, respectively, creating a 1.9 kbp product. The forward primer incorporates a Xbal restriction site and a RBS. The reverse primer incorporates a BamHI restriction site. The PCR product is cloned into pCR4 Blunt-TOPO creating pCR4 Blunt-TOPO-ilvD. Plasmid DNA is prepared from the TOPO clones and the sequence of the gene is verified. The kivD gene is amplified from pUC57-kivD (described in Example 8) by PCR using primer pair N116 and N117 (see Table 2), given as SEQ ID NOs:25 and 26, respectively, creating a 1.7 bp product. The forward primer incorporates a BamHI restriction site and a RBS. The reverse primer incorporates a Sacl restriction site. The PCR product is cloned into pCR4 Blunt-TOPO creating pCR4 Blunt-TOPO-kivD. Plasmid DNA is prepared from the TOPO clones and the sequence of the gene is verified. The yqhD gene is amplified from E. coli K12 genomic DNA by PCR using primer pair N118 and N119 (see Table 2) given as SEQ ID NOs:27 and 28, respectively, creating a 1.2 kbp product. The forward primer incorporates a Sacl restriction site. The reverse primer incorporates Spel and EcoRI restriction sites. The PCR product is cloned into pCR4 Blunt- TOPO creating pCR4 Blunt-TOPO-yqhD. Plasmid DNA is prepared from the TOPO clones and the sequence of the gene is verified.
To construct the isobutanol pathway operon, the yqhD gene is excised from pCR4 Blunt-TOPO-yqftD with Sacl and EcoRI, releasing a 1.2 kbp fragment. This is ligated with pUC19dHS, which has previously been digested with Sacl and EcoRI. The resulting clone, pUC19dHS- yqhD, is confirmed by restriction digest. Next, the HvC gene is excised from pCR4 Blunt-TOPO-ilvC with Sail and Xbal, releasing a 1.5 kbp fragment. This is ligated with pUC19dHS-yqhD, which has previously been digested with Sail and Xbal. The resulting clone, pUC19dHS-ilvC- yqhD, is confirmed by restriction digest. The budB gene is then excised from pCR4 BIunt-TOPO-buc/B with Sphl and Nsil, releasing a 1.8 kbp fragment. pUC19dHS-ilvC-yqhD is digested with Sphl and Pstl and ligated with the Sphl/Nsil budB fragment (Nsil and Pstl generate compatible ends), forming pUC19dHS-budB-ilvC-yqhD. A 1.9 kbp fragment containing the HvD gene is excised from pCR4 Blunt-TOPO-ilvD with Xbal and BamHI and ligated with pUC19dHS-budB-ilvC-yqhD, which is digested with these same enzymes, forming pUC19dHS-budB-ilvC-ilvD- yqhD. Finally, kivD is excised from pCR4 Blunt-TOPO-kivD with BamHI and Sacl, releasing a 1.7 kbp fragment. This fragment is ligated with pUC19dHS-budB-ilvC-ilvD-yqhD, which has previously been digested with BamHI and Sacl, forming pUC19dHS-budB-ilvC-ilvD-kivD-yqhD.
The pUC19dHS-budB-ilvC-ilvD-kivD-yqhD vector is digested with AfIII and Spel to release a 8.2 kbp operon fragment that is cloned into pBenAS, an E.coli-B. subtilis shuttle vector. Plasmid pBenAS is created by modification of the pBE93 vector, which is described by Nagarajan, (WO 93/24631 , Example 4). To make pBenAS the Bacillus amyloliquefaciens neutral protease promoter (NPR), signal sequence, and the phoA gene are removed with a Ncol/Hindlll digest of pBE93. The NPR promoter is PCR amplified from pBE93 by primers BenNF and BenASR, given as SEQ ID NOS:29 and 30, respectively. Primer BenASR incorporates AfIII, Spel, and Hindlll sites downstream of the promoter. The PCR product is digested with Ncol and Hindlll and the fragment is cloned into the corresponding sites in the vector creating pBenAS. The operon fragment is subcloned into the AfIII and Spel sites in pBenAS creating pBen-budB- ilvC-ilvD-kivD-yqhD.
EXAMPLE 11 (Prophetic) Expression of the lsobutanol Biosynthetic Pathway in E. coli The purpose of this prophetic Example is to describe how to express an isobutanol biosynthetic pathway in E. coli.
The plasmid pBen-budB-ilvC-ilvD-kivD-yqhD, constructed as described in Example 10, is transformed into E. coli NM522 (ATCC No. 47000) to give E. coli strain NM522/pBen-budB-ilvC-ilvD-kivD-yqhD and expression of the genes in the operon is monitored by SDS-PAGE analysis, enzyme assay and Western blot analysis. For Western blots, antibodies are raised to synthetic peptides by Sigma-Genosys (The Woodlands, TX).
E. coli strain NM522/pBen-budB-ilvC-ilvD-kivD-yqhD is inoculated into a 250 ml_ shake flask containing 50 ml_ of medium and shaken at 250 rpm and 35 0C. The medium is composed of: glucose (5 g/L), MOPS (0.05 M), ammonium sulfate (0.01 M), potassium phosphate, monobasic (0.005 M), S10 metal mix (1 % (v/v)) yeast extract (0.1 % (w/v)), casamino acids (0.1 % (w/v)), thiamine (0.1 mg/L), proline (0.05 mg/L), and biotin (0.002 mg/L), and is titrated to pH 7.0 with KOH. S10 metal mix contains: MgCI2 (200 mM), CaCI2 (70 mM), MnCI2 (5 mM), FeCI3 (0.1 mM), ZnCI2 (0.1 mM), thiamine hydrochloride (0.2 mM), CuSO4 (172 μM), CoCI2 (253 μM), and Na2MoO4 (242 μM). After 18 h, isobutanol is detected by HPLC or GC analysis, using methods that are well known in the art, for example, as described in the General Methods section above. EXAMPLE 12 (Prophetic) Expression of the lsobutanol Biosynthetic Pathway in Bacillus subtilis
The purpose of this prophetic Example is to describe how to express an isobutanol biosynthetic pathway in Bacillus subtilis. The same approach as described in Example 11 is used.
The plasmid pBen-budB-ilvC-ilvD-kivD-yqhD, constructed as described in Example 10, is used. This plasmid is transformed into Bacillus subtilis BE1010 (J. Bacteriol. 173:2278-2282 (1991 )) to give B. subtilis strain BE1010/pBen-budB-ilvC-ilvD-kivD-yqhD and expression of the genes in each operon is monitored as described in Example 11.
B. subtilis strain BE1010/pBen-budB-ilvC-ilvD-kivD-yqhD is inoculated into a 250 ml_ shake flask containing 50 ml_ of medium and shaken at 250 rpm and 35 0C for 18 h. The medium is composed of: dextrose (5 g/L), MOPS (0.05 M), glutamic acid (0.02 M), ammonium sulfate (0.01 M), potassium phosphate, monobasic buffer (0.005 M), S10 metal mix (as described in Example 11 , 1 % (v/v)), yeast extract (0.1 % (w/v)), casamino acids (0.1 % (w/v)), tryptophan (50 mg/L), methionine (50 mg/L), and lysine (50 mg/L), and is titrated to pH 7.0 with KOH. After 18 h, isobutanol is detected by HPLC or GC analysis using methods that are well known in the art, for example, as described in the General Methods section above.
EXAMPLE 13
Cloning and Expression of Acetolactate Synthase To create another acetolactate synthase expression clone, the budB gene was cloned into the vector pTrc99A. The budB gene was first amplified from pENTRSDD-TOPObudB (described in Example 5) using primers (N110.2 and N111.2, given as SEQ ID NOs:31 and 32, respectively) that introduced Sac\, Spe\ and Mfe\ sites at the 5' end and BbvC\, AfIW, and BamH\ sites at the 3' end. The resulting 1.75 kbp PCR product was cloned into pCR4-Blunt TOPO (Invitrogen) and the DNA sequence was confirmed (using N130Seq sequencing primers F1-F4 and R1 -R4, given as SEQ ID NOs:40-47, respectively). The budB gene was then excised from this vector using Sac\ and BamH\ and cloned into pTrc99A (Amann et al. Gene 69(2):301 -315 (1988)), generating pTrc99A::budB. The pTrc99A::budB vector was transformed into E. coli TOP10 cells and the transformants were inoculated into LB medium supplemented with 50 μg/mL of ampicillin and grown overnight at 37 0C. An aliquot of the overnight culture was used to inoculate 50 ml_ of LB medium supplemented with 50 μg/mL of ampicillin. The culture was incubated at 37 0C with shaking until the OD6oo reached 0.6 to 0.8. Expression of budB from the Trc promoter was then induced by the addition of 0.4 mM IPTG. Negative control flasks were also prepared that were not induced with IPTG. The flasks were incubated for 4 h at 37 0C with shaking. Cell-free extracts were prepared as described in Example 5.
Acetolactate synthase activity in the cell free extracts was measured as described in Example 5. Three hours after induction with IPTG, an acetolactate synthase activity of 8 units/mg was detected. The control strain carrying only the pTrc99A plasmid exhibited 0.03 units/mg of acetolactate synthase activity.
EXAMPLE 14 Cloning and Expression of Acetohvdroxy Acid Reductoisomerase
The purpose of this Example was to clone the HvC gene from E. coli K12 and express it in E. coli TOP10. The HvC gene was amplified from E. coli K12 strain FM5 (ATCC 53911 ) genomic DNA using PCR.
The HvC gene was cloned and expressed in a similar manner as described for the cloning and expression of HvC in Example 6 above. PCR was used to amplify HvC from the E. coli FM5 genome using primers N112.2 and N113.2 (SEQ ID NOs:33 and 34, respectively). The primers created Sac\ and AfIIW sites and an optimal RBS at the 5' end and Not\, Nhe\ and BamH\ sites at the 3' end of HvC. The 1.5 kbp PCR product was cloned into pCR4Blunt TOPO according to the manufacturer's protocol (Invitrogen) generating pCR4Blunt TOPO::ilvC. The sequence of the PCR product was confirmed using sequencing primers (N131 SeqF1 -F3, and N131 SeqR1 -R3, given as SEQ ID NOs:48-53, respectively). To create an expression clone, the HvC gene was excised from pCR4Blunt TOPO::ilvC using Sac\ and BamH\ and cloned into pTrc99A. The pTrc99A::ilvC vector was transformed into E. coli TOP10 cells and expression from the Trc promoter was induced by addition of IPTG, as described in Example 13. Cell-free extracts were prepared as described in Example 5.
Acetohydroxy acid reductoisomerase activity in the cell free extracts was measured as described in Example 6. Three hours after induction with IPTG, an acetohydroxy acid reductoisomerase activity of 0.026 units/mg was detected. The control strain carrying only the pTrc99A plasmid exhibited less than 0.001 units/mg of acetohydroxy acid reductoisomerase activity.
EXAMPLE 15 Cloning and Expression of Acetohvdroxy Acid Dehydratase
The purpose of this Example was to clone the HvD gene from E. coli K12 and express it in E. coli Top10. The HvD gene was amplified from E. coli K12 strain FM5 (ATCC 53911 ) genomic DNA using PCR.
The HvD gene was cloned and expressed in a similar manner as the HvC gene described in Example 14. PCR was used to amplify HvD from the E. coli FM5 genome using primers N114.2 and N115.2 (SEQ ID NOs:35 and 36, respectively). The primers created Sac\ and Nhe\ sites and an optimal RBS at the 5' end and Bsu36\, Pac\ and BamH\ sites at the 3' end of HvD. The 1.9 kbp PCR product was cloned into pCR4Blunt TOPO according to the manufacturer's protocol (Invitrogen) generating pCR4Blunt TOPO::ilvD. The sequence of the PCR product was confirmed (sequencing primers N132SeqF1-F4 and N132SeqR1 -R4, given as SEQ ID NOs:54-61 , respectively). To create an expression clone, the HvD gene was excised from plasmid pCR4Blunt TOPO::ilvD using Sac\ and BamH\, and cloned into pTrc99A. The pTrc99A::ilvD vector was transformed into E. coli TOP10 cells and expression from the Trc promoter was induced by addition of IPTG, as described in Example 13. Cell-free extracts were prepared as described in Example 5.
Acetohydroxy acid dehydratase activity in the cell free extracts was measured as described in Example 7. Three hours after induction with IPTG, an acetohydroxy acid dehydratase activity of 46 units/mg was measured. The control strain carrying only the pTrc99A plasmid exhibited no detectable acetohydroxy acid dehydratase activity. EXAMPLE 16 Cloning and Expression of Branched-Chain Keto Acid Decarboxylase
The purpose of this Example was to clone the kivD gene from Lactococcus lactis and express it in E. coli TOP10. The kivD gene was cloned and expressed in a similar manner as that described for HvC in Example 14 above. PCR was used to amplify /c/VD from the plasmid pUC57-kivD (see Example 8, above) using primers N116.2 and N117.2 (SEQ ID NOs:37 and 38, respectively). The primers created Sac\ and Pac\ sites and an optimal RBS at the 5' end and Pci\, AvrW, BgIW and BamH\ sites at the 3' end of kivD. The 1.7 kbp PCR product was cloned into pCR4Blunt TOPO according to the manufacturer's protocol (Invitrogen) generating pCR4Blunt TOPO::kivD. The sequence of the PCR product was confirmed using primers N133SeqF1-F4 and N133SeqR1 -R4 (given as SEQ ID NOs:62-69, respectively). To create an expression clone, the kivD gene was excised from plasmid pCR4Blunt TOPO::kivD using Sac\ and BamH\, and cloned into pTrc99A. The pTrc99A::kivD vector was transformed into E. coli TOP10 cells and expression from the Trc promoter was induced by addition of IPTG, as described in Example 13. Cell-free extracts were prepared as described in Example 5.
Branched-chain keto acid decarboxylase activity in the cell free extracts was measured as described in Example 8, except that Purpald® reagent (Aldrich, Catalog No. 162892) was used to detect and quantify the aldehyde reaction products. Three hours after induction with IPTG, a branched-chain keto acid decarboxylase activity of greater than 3.7 units/mg was detected. The control strain carrying only the pTrc99A plasmid exhibited no detectable branched-chain keto acid decarboxylase activity.
EXAMPLE 17 Expression of Branched-Chain Alcohol Dehydrogenase
E. coli contains a native gene {yqhD) that was identified as a 1 ,3- propanediol dehydrogenase (U.S. Patent No. 6,514,733). The YqhD protein has 40% identity to AdhB (encoded by adhB) from Clostridium, a putative NADH-dependent butanol dehydrogenase. The yqhD gene was placed under the constitutive expression of a variant of the glucose isomerase promoter 1.6Gl (SEQ ID NO. 70) in E. coli strain MG1655 1.6yqhD::Cm (WO 2004/033646) using λ Red technology (Datsenko and Wanner, Proc. Natl. Acad. Sci. U.S.A. 97:6640 (2000)). MG1655 1.6yqhD::Cm contains a FRT-CmR-FRT cassette so that the antibiotic marker can be removed. Similarly, the native promoter was replaced by the 1.5Gl promoter (WO 2003/089621 ) (SEQ ID NO. 71 ), creating strain MG1655 1.5GI-yqhD::Cm, thus, replacing the 1.6Gl promoter of MG1655 1.6yqhD::Cm with the 1.5Gl promoter. Strain MG1655 1.5GI-yqhD::Cm was grown in LB medium to mid- log phase and cell free extracts were prepared as described in Example 5. This strain was found to have NADPH-dependent isobutyraldehyde reductase activity when the cell extracts were assayed by following the decrease in absorbance at 340 nm at pH 7.5 and 35 0C. To generate a second expression strain containing 1.5Gl yqhD::Cm, a P1 lysate was prepared from MG1655 1.5Gl yqhD::Cm and the cassette was transferred to BL21 (DE3) (Invitrogen) by transduction, creating BL21 (DE3) 1.5GI-yqhD::Cm.
EXAMPLE 18 Construction of a Transformation Vector for the First Four
Genes in an lsobutanol Biosvnthetic Pathway The purpose of this Example was to construct a transformation vector comprising the first four genes (i.e., budB, HvC, HvD and kivD) in an isobutanol biosynthetic pathway. To construct the transformation vector, first, the HvC gene was obtained from pTrc99A::ilvC (described in Example 14) by digestion with AfIW and BamH\ and cloned into pTrc99A::budB (described in Example 13), which was digested with AfIW and BamH\ to produce plasmid pTrc99A::budB-ilvC. Next, the HvD and kivD genes were obtained from pTrc99A::ilvD (described in Example 15) and pTrc99A::kivD (described in Example 16), respectively, by digestion with Nhe\ and Pac\ (HvD) and Pac\ and BamH\ (kivD). These genes were introduced into pTrc99A::budB- ilvC,which was first digested with Nhe\ and BamH\, by three-way ligation. The presence of all four genes in the final plasmid, pTrc99A::budB-ilvC- ilvD-kivD, was confirmed by PCR screening and restriction digestion.
EXAMPLE 19
Expression of an lsobutanol Biosynthetic Pathway in E. coli Grown on Glucose
To create E. coli isobutanol production strains, pTrc99A::budB-ilvC- ilvD-kivD (described in Example 18) was transformed into E. coli MG1655 1.5Gl yqhD::Cm and E. coli B L21 (DE3) 1.5Gl yqhD::Cm (described in Example 17). Transformants were initially grown in LB medium containing 50 μg/mL kanamycin and 100 μg/mL carbenicillin. The cells from these cultures were used to inoculate shake flasks (approximately 175 mL total volume) containing 50 or 170 mL of TM3a/glucose medium (with appropriate antibiotics) to represent high and low oxygen conditions, respectively. TM3a/glucose medium contained (per liter): glucose (10 g), KH2PO4 (13.6 g), citric acid monohydrate (2.0 g), (NH4)2SO4 (3.0 g),
MgSO4TH2O (2.0 g), CaCI2-2H2O (0.2 g), ferric ammonium citrate (0.33 g), thiamine HCI (1.0 mg), yeast extract (0.50 g), and 10 mL of trace elements solution. The pH was adjusted to 6.8 with NH4OH. The trace elements solution contained: citric acid H2O (4.0 g/L), MnSO4-H2O (3.0 g/L), NaCI (1.0 g/L), FeSO4-7H2O (0.10 g/L), CoCI2-6H2O (0.10 g/L), ZnSO4-7H2O (0.10 g/L), CuSO4-5H2O (0.010 g/L), H3BO3 (0.010 g/L), and Na2Moθ4- 2H2O (0.010 g/L).
The flasks were inoculated at a starting OD6oo of < 0.01 units and incubated at 34 0C with shaking at 300 rpm. The flasks containing 50 mL of medium were closed with 0.2 μm filter caps; the flasks containing 150 mL of medium were closed with sealed caps. IPTG was added to a final concentration of 0.04 mM when the cells reached an OD6oo of > 0.4 units. Approximately 18 h after induction, an aliquot of the broth was analyzed by HPLC (Shodex Sugar SH1011 column (Showa Denko America, Inc. NY) with refractive index (Rl) detection) and GC (Varian CP-WAX 58(FFAP) CB, 0.25 mm X 0.2 μm X 25 m (Varian, Inc., Palo Alto, CA) with flame ionization detection (FID)) for isobutanol content, as described in the General Methods section. No isobutanol was detected in control strains carrying only the pTrc99A vector (results not shown). Molar selectivities and titers of isobutanol produced by strains carrying pTrc99A::budB-ilvC- ilvD-kivD are shown in Table 13. Significantly higher titers of isobutanol were obtained in the cultures grown under low oxygen conditions.
Table 13 Production of Isobutanol by E. coli Strains Grown on Glucose
Figure imgf000087_0001
*Determined by HPLC.
EXAMPLE 20 Expression of an Isobutanol Biosynthetic Pathway in E. coli Grown on
Sucrose
Since the strains described in Example 19 were not capable of growth on sucrose, an additional plasmid was constructed to allow utilization of sucrose for isobutanol production. A sucrose utilization gene cluster cscBKA, given as SEQ ID NO:39, was isolated from genomic DNA of a sucrose-utilizing E. coli strain derived from ATCC strain 13281. The sucrose utilization genes (cscA, cscK, and cscB) encode a sucrose hydrolase (CscA), given as SEQ ID NO:139, D-fructokinase (CscK), given as SEQ ID NO:140, and sucrose permease (CscB), given as SEQ ID NO:141. The sucrose-specific repressor gene cscR was not included so that the three genes cscBKA were expressed constitutively from their native promoters in E. coli.
Genomic DNA from the sucrose-utilizing E. coli strain was digested to completion with BamH\ and EcoR\. Fragments having an average size of about 4 kbp were isolated from an agarose gel and were ligated to plasmid pLitmus28 (New England Biolabs), digested with BamH\ and EcoR\ and transformed into ultracompetent E. co// TOP10F' cells (Invitrogen). The transformants were streaked onto MacConkey agar plates containing 1 % sucrose and ampicillin (100 μg/mL) and screened for the appearance of purple colonies. Plasmid DNA was isolated from the purple transformants, and sequenced with M13 Forward and Reverse primers (Invitrogen), and Scr1 -4 (given as SEQ ID NOs:72-75, respectively). The plasmid containing cscB, cscK, and cscA (cscBKA) genes was designated pScr1. To create a sucrose utilization plasmid that was compatible with the isobutanol pathway plasmid (Example 18), the operon from pScri was subcloned into pBHR1 (MoBiTec, Goettingen, Germany). The cscBKA genes were isolated by digestion of pScri with Xho\ (followed by incubation with Klenow enzyme to generate blunt ends) and then by digestion with Age\. The resulting 4.2 kbp fragment was ligated into pBHR1 that had been digested with Λ/ael and Age\, resulting in the 9.3 kbp plasmid pBHR1 ::cscBKA.
The sucrose plasmid pBHR1 ::cscBKA was transformed into E. coli BL21 (DE3) 1.5 yqhD /pTrc99A::budB-ilvC-ilvD-kivD and E. coli MG1655 1.5yqhD /pTrc99A::budB-ilvC-ilvD-kivD (described in Example 19) by electroporation. Transformants were first selected on LB medium containing 100 μg/mL ampicillin and 50 μg/mL kanamycin and then screened on MacConkey sucrose (1 %) plates to confirm functional expression of the sucrose operon. For production of isobutanol, strains were grown in TM3a minimal defined medium (described in Example 19) containing 1 % sucrose instead of glucose, and the culture medium was analyzed for the amount of isobutanol produced, as described in Example 19, except that samples were taken 14 h after induction. Again, no isobutanol was detected in control strains carrying only the pTrc99A vector (results not shown). Molar selectivities and titers of isobutanol produced by MG1655 1.5yqhD carrying pTrc99A::budB-ilvC-ilvD-kivD are shown in Table 14. Similar results were obtained with the analogous BL21 (DE3) strain.
Table 14
Production of Isobutanol by E. coli strain MG1655 1.δvqhD /pTrc99A:: budB-ilvC-ilvD-kivD/pBHRI ::cscBKA Grown on Sucrose
Figure imgf000089_0001
*Determined by HPLC.
EXAMPLE 21
Expression of Isobutanol Pathway Genes in Saccharomyces Cerevisiae To express isobutanol pathway genes in Saccharomyces cerevisiae, a number of E. co//-yeast shuttle vectors were constructed. A PCR approach (Yu, et al. Fungal Genet. Biol. 41 :973-981 (2004)) was used to fuse genes with yeast promoters and terminators. Specifically, the GPD promoter (SEQ ID NO:76) and CYC1 terminator (SEQ ID NO:77) were fused to the alsS gene from Bacillus subtilis (SEQ ID NO:78), the FBA promoter (SEQ ID NO:79) and CYC1 terminator were fused to the ILV5 gene from S. cerevisiae (SEQ ID NO:80), the ADH1 promoter (SEQ ID NO:81 ) and ADH 1 terminator (SEQ ID NO:82) were fused to the ILV3 gene from S. cerevisiae (SEQ ID NO:83), and the GPM promoter (SEQ ID NO:84) and ADH 1 terminator were fused to the kivD gene from Lactococcus lactis (SEQ ID NO:7). The primers, given in Table 15, were designed to include restriction sites for cloning promoter/gene/terminator products into E. co//-yeast shuttle vectors from the pRS400 series (Christianson et al. Gene 110:119-122 (1992)) and for exchanging promoters between constructs. Primers for the 5' ends of ILV5 and ILV3 (N138 and N155, respectively, given as SEQ ID NOs: 95 and 107, respectively) generated new start codons to eliminate mitochondrial targeting of these enzymes.
All fused PCR products were first cloned into pCR4-Blunt by TOPO cloning reaction (Invitrogen) and the sequences were confirmed (using M13 forward and reverse primers (Invitrogen) and the sequencing primers provided in Table 15. Two additional promoters (CUP1 and GAL1 ) were cloned by TOPO reaction into pCR4-Blunt and confirmed by sequencing; primer sequences are indicated in Table 15. The plasmids that were constructed are described in Table 16. The plasmids were transformed into either Saccharomyces cerevisiae BY4743 (ATCC 201390) or YJR148w (ATCC 4036939) to assess enzyme specific activities using the enzyme assays described in Examples 5-8 and Examples 13-16. For the determination of enzyme activities, cultures were grown to an OD600 of
1.0 in synthetic complete medium (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 201 -202) lacking any metabolite(s) necessary for selection of the expression plasmid(s), harvested by centhfugation (2600 x g for 8 min at 4 0C), washed with buffer, centrifuged again, and frozen at -80 0C. The cells were thawed, resuspended in 20 mM Tris-HCI, pH 8.0 to a final volume of 2 ml_, and then disrupted using a bead beater with 1.2 g of glass beads (0.5 mm size). Each sample was processed on high speed for 3 minutes total (with incubation on ice after each minute of beating). Extracts were cleared of cell debris by centrifugation (20,000 x g for 10 min at 4 0C).
Table 15
Primer Sequences for Cloning and Sequencing of S. cerevisiae Expression Vectors
Figure imgf000090_0001
Figure imgf000091_0001
Figure imgf000092_0001
Figure imgf000093_0001
Figure imgf000094_0001
Figure imgf000095_0001
Table 16 E. co//- Yeast Shuttle Vectors Carrying lsobutanol Pathway Genes
Figure imgf000095_0002
Figure imgf000096_0001
EXAMPLE 22 Production of lsobutanol by Recombinant Saccharomyces Cerevisiae
Plasmids pRS423::CUP1 -alsS+FBA-ILV3 and pHR81 ::FBA- ILV5+GPM-kivD (described in Example 21 ) were transformed into Saccharomyces cerevisiae YJR148w to produce strain YJR148w/pRS423::CUP1 -alsS+FBA-ILV3/ pHR81 ::FBA-ILV5+ GPM-kivD. A control strain was prepared by transforming vectors pRS423 and pHR81 (described in Example 21 ) into Saccharomyces cerevisiae YJR148w (strain YJR148w/pRS423/pHR81 ). Strains were maintained on standard S. cerevisiae synthetic complete medium (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 201 -202) containing either 2% glucose or sucrose but lacking uracil and histidine to ensure maintenance of plasmids. For isobutanol production, cells were transferred to synthetic complete medium lacking uracil, histidine and leucine. Removal of leucine from the medium was intended to trigger an increase in copy number of the pHR81 -based plasmid due to poor transcription of the Ieu2-d allele (Erhart and Hollenberg, J. Bacteriol. 156:625-635 (1983)). Aerobic cultures were grown in 175 ml_ capacity flasks containing 50 ml_ of medium in an Innova4000 incubator (New Brunswick Scientific, Edison, NJ) at 30 0C and 200 rpm. Low oxygen cultures were prepared by adding 45 ml_ of medium to 60 ml_ serum vials that were sealed with crimped caps after inoculation and kept at 30 0C. Sterile syringes were used for sampling and addition of inducer, as needed. Approximately 24 h after inoculation, the inducer CuSO4was added to a final concentration of 0.03 mM. Control cultures for each strain without CuSO4 addition were also prepared. Culture supernatants were analyzed 18 or 19 h and 35 h after CuSO4 addition by both GC and HPLC for isobutanol content, as described above in Example 19. The results for S. cerevisiae YJR148w/pRS423::CUP1 -alsS+FBA- ILV3/pHR81 ::FBA-ILV5+GPM-kivD grown on glucose are presented in Table 17. For the results given in Table 17, the samples from the aerobic cultures were taken at 35 h and the samples from the low oxygen cultures were taken at 19 h and measured by HPLC.
The results for S. cerevisiae YJR148w/pRS423::CUP1 -alsS+FBA- ILV3/pHR81 ::FBA-ILV5+GPM-kivD grown on sucrose are presented in Table 18. The results in this table were obtained with samples taken at 18 h and measured by HPLC.
Table 17
Production of Isobutanol by S. cerevisiae YJR148w/pRS423::CUP1- alsS+FBA-ILV3/pHR81 ::FBA-ILV5+GPM-kivD Grown on Glucose
Figure imgf000097_0001
Figure imgf000098_0001
Table 18
Production of lsobutanol by S. cerevisiae YJR148w/pRS423::CUP1- alsS+FBA-ILV3/pHR81 ::FBA-ILV5+GPM-kivD Grown on Sucrose
Figure imgf000098_0002
Strain suffixes "a", "b", and "c" indicate separate isolates. The results indicate that, when grown on glucose or sucrose under both aerobic and low oxygen conditions, strain YJR148w/pRS423::CUP1 - alsS+FBA-ILV3/ pHR81 ::FBA-ILV5+ GPM-kivD produced consistently higher levels of isobutanol than the control strain.
EXAMPLE 23 Production of Isobutanol by Recombinant Saccharomyces Cerevisiae
Plasmids pRS425::CUP1 -alsS+FBA-ILV3 and pRS426::GAL1- ILV5+GPM-kivD (described in Example 21 ) were transformed into Saccharomyces cerevisiae YJR148w to produce strain
YJR148w/pRS425::CUP1 -alsS+ FBA-ILV3/pRS426::GAL1 -ILV5+ GPM- kivD. A control strain was prepared by transforming vectors pRS425 and pRS426 (described in Example 21 ) into Saccharomyces cerevisiae YJR148w (strain YJR148w/pRS425/pRS426). Strains were maintained on synthetic complete medium, as described in Example 22.
For isobutanol production, cells were transferred to synthetic complete medium containing 2% galactose and 1 % raffinose, and lacking uracil and leucine. Aerobic and low oxygen cultures were prepared as described in Example 22. Approximately 12 h after inoculation, the inducer CuSO4 was added up to a final concentration of 0.5 mM. Control cultures for each strain without CuSO4 addition were also prepared. Culture supernatants were sampled 23 h after CuSO4 addition for determination of isobutanol by HPLC, as described in Example 22. The results are presented in Table 19. Due to the widely different final optical densities observed and associated with quantifying the residual carbon source, the concentration of isobutanol per OD600 unit (instead of molar selectivities) is provided in the table to allow comparison of strains containing the isobutanol biosynthetic pathway genes with the controls. Table 19
Production of lsobutanol by S. cerevisiae YJR148w/pRS425::CUP1- alsS+FBA-ILV3/pRS426::GAL1 -ILV5+GPM-kivD Grown on Galactose and
Raffinose
Figure imgf000100_0001
Figure imgf000101_0001
Strain suffixes "a", "b", "c", "d" and "e" indicate separate isolates.
The results indicate that in general, higher levels of isobutanol per optical density unit were produced by the YJR148w/pRS425::CUP1 -alsS+ FBA-ILV3/pRS426::GAL1 -ILV5+ GPM-kivD strain compared to the control strain under both aerobic and low oxygen conditions.
EXAMPLE 24 Expression of an Isobutanol Biosynthetic Pathway in Bacillus subtilis
The purpose of this Example was to express an isobutanol biosynthetic pathway in Bacillus subtilis. The five genes of the isobutanol pathway (pathway steps (a) through (e) in Figure 1 ) were split into two operons for expression. The three genes budB, HvD, and kivD, encoding acetolactate synthase, acetohydroxy acid dehydratase, and branched- chain keto acid decarboxylase, respectively, were integrated into the chromosome of B. subtilis BE1010 (Payne and Jackson, J. Bacteriol. 173:2278-2282 (1991 )). The two genes HvC and bdhB, encoding acetohydroxy acid isomeroreductase and butanol dehydrogenase, respectively, were cloned into an expression vector and transformed into the Bacillus strain carrying the integrated isobutanol genes.
Integration of the three genes, budB, HvD and kivD into the chromosome of B. subtilis BE1010. Bacillus integration vectors pFP988DssPspac and pFP988DssPgroE were used for the chromosomal integration of the three genes, budB (SEQ ID NO:1 ), HvD (SEQ ID NO:5), and kivD (SEQ ID NO:7). Both plasmids contain an E. coli replicon from pBR322, an ampicillin antibiotic marker for selection in E. coli and two sections of homology to the sacB gene in the Bacillus chromosome that direct integration of the vector and intervening sequence by homologous recombination. Between the sacB homology regions is a spac promoter (PgroE) on pFP988DssPspac or a groEL promoter (PgroE) on pFP988DssPgroE, and a selectable marker for Bacillus, erythromycin. The promoter region also contains the lacO sequence for regulation of expression by a lacl repressor protein. The sequences of pFP988DssPspac (6,341 bp) and pFP988DssPgroE (6,221 bp) are given as SEQ ID NO:142 and SEQ ID NO:143 respectively.
The cassette with three genes budB-ilvD-kivD was constructed by deleting the HvC gene from plasmid pTrc99a budB-ilvC-ilvD-kivD. The construction of the plasmid pTrc99A::budB-ilvC-ilvD-kivD is described in Example 18. Plasmid pTrc99A::budB-ilvC-ilvD-kivD was digested with AfIII and Nhel, treated with the Klenow fragment of DNA polymerase to make blunt ends, and the resulting 9.4 kbp fragment containing pTrc99a vector, budB, HvD, and kivD was gel-purified. The 9.4 kbp vector fragment was self-ligated to create pTrc99A::budB-ilvD-kivD, and transformed into DH5α competent cells (Invitrogen). A clone of pTrc99a budB-ilvD-kivD was confirmed for the HvC gene deletion by restriction mapping. The resulting plasmid pTrc99A::budB-ilvD-kivD was digested with Sacl and treated with the Klenow fragment of DNA polymerase to make blunt ends. The plasmid was then digested with BamHI and the resulting 5,297 bp budB-ilvD-kivD fragment was gel-purified. The 5,297 bp budB-ilvD-kivD fragment was ligated into the Smal and BamHI sites of the integration vector pFP988DssPspac. The ligation mixture was transformed into DH5α competent cells. Transformants were screened by PCR amplification of the 5.3 kbp budB-ilvD-kivD fragment with primers T-budB(BamHI) (SEQ ID NO:144) and B-kivD(BamHI) (SEQ ID NO:145). The correct clone was named pFP988DssPspac-budB-ilvD-kivD.
Plasmid pFP988DssPspac-budB-ilvD-kivD was prepared from the E. coli transformant, and transformed into B. subtilis BE1010 competent cells, which had been prepared as described by Doyle et al. (J. Bacteriol. 144:957 (1980)). Competent cells were harvested by centrifugation and the cell pellets were resuspended in a small volume of the supernatant. To one volume of competent cells, two volumes of SPII-EGTA medium (Methods for General and Molecular Bacteriology, P. Gerhardt et al., Ed., American Society for Microbiology, Washington, DC (1994)) was added. Aliquots (0.3 ml_) of cells were dispensed into test tubes and then 2 to 3 μg of plasmid pFP988DssPspac-budB-ilvD-kivD was added to the tubes. The tubes were incubated for 30 min at 37 0C with shaking, after which 0.1 ml_ of 10% yeast extract was added to each tube and they were further incubated for 60 min. Transformants were grown for selection on LB plates containing erythromycin (1.0 μg/mL) using the double agar overlay method (Methods for General and Molecular Bacteriology, supra). Transformants were screened by PCR amplification with primers N130SeqF1 (SEQ ID NO:40) and N130SeqR1 (SEQ ID NO:44) for budB, and N133SeqF1 (SEQ ID NO:62) and N133SeqR1 (SEQ ID NO:66) for kivD. Positive integrants showed the expected 1.7 kbp budB and 1.7 kbp kivD PCR products. Two positive integrants were identified and named B. subtilis BE1010 ΔsacB::Pspac-budB-ilvD-kivD #2-3-2 and B. subtilis BE1010 ΔsacB::Pspac-budB-ilvD-kivD #6-12-7. Assay of the enzyme activities in integrants B. subtilis BE1010
ΔsacB::Pspac-budB-ilvD-kivD #2-3-2 and B. subtilis BE1010 ΔsacB::Pspac-budB-ilvD-kivD #6-12-7 indicated that the activities of BudB, HvD and KivD were low under the control of the spac promoter (Pspac). To improve expression of functional enzymes, the Pspac promoter was replaced by a PgroE promoter from plasmid pHT01 (MoBitec, Goettingen, Germany).
A 6,039 bp pFP988Dss vector fragment, given as SEQ ID NO:146, was excised from an unrelated plasmid by restriction digestion with Xhol and BamHI, and was gel-purified. The PgroE promoter was PCR- amplified from plasmid pHT01 with primers T-groE(Xhol) (SEQ ID
NO:147) and B-groEL(Spel, BamHI ) (SEQ ID NO:148). The PCR product was digested with Xhol and BamHI, ligated with the 6,039 bp pFP988Dss vector fragment, and transformed into DH5α competent cells. Transformants were screened by PCR amplification with primers T- groE(Xhol) and B-groEL(Spel,BaιτιH1 ). Positive clones showed the expected 174 bp PgroE PCR product and were named pFP988DssPgroE. The plasmid pFP988DssPgroE was also confirmed by DNA sequence. Plasmid pFP988DssPspac-budB-ilvD-kivD was digested with Spel and Pmel and the resulting 5,313 bp budB-ilvD-kivD fragment was gel- purified. The budB-ilvD-kivD fragment was ligated into Spel and Pmel sites of pFP988DssPgroE and transformed into DH5α competent cells. Positive clones were screened for a 1 ,690 bp PCR product by PCR amplification with primers T-groEL (SEQ ID NO:149) and N111 (SEQ ID NO:20). The positive clone was named pFP988DssPgroE-budB-ilvD-kivD.
Plasmid pFP988DssPgroE-budB-ilvD-kivD was prepared from the E. coli transformant, and transformed into Bacillus subtilis BE1010 competent cells as described above. Transformants were screened by PCR amplification with primers N130SeqF1 (SEQ ID NO:40) and
N130SeqR1 (SEQ ID NO:44) for budB, and N133SeqF1 (SEQ ID NO:62) and N133SeqR1 (SEQ ID NO:66) for kivD. Positive integrants showed the expected 1.7 kbp budB and 1.7 kbp kivD PCR products. Two positive integrants were isolated and named B. subtilis BE1010 ΔsacB::PgroE- budB-ilvD-kivD #1 -7 and B. subtilis BE1010 ΔsacB::PgroE-budB-ilvD-kivD #8-16.
Plasmid Expression of HvC and bdhB genes. Two remaining isobutanol genes, HvC and bdhB, were expressed from a plasmid. Plasmid pHT01 (MoBitec), a Bacillus-E. coli shuttle vector, was used to fuse an HvC gene from B. subtilis to a PgroE promoter so that the HvC gene was expressed from the PgroE promoter containing a lacO sequence. The HvC gene, given as SEQ ID NO:186, was PCR-amplified from B. subtilis BR151 (ATCC 33677) genomic DNA with primers T-ilvCB.s.(BamHI) (SEQ ID NO:150) and B-ilvCB.s.(Spel BamHI) (SEQ ID NO:151 ). The 1 ,067 bp HvC PCR product was digested with BamHI and ligated into the BamHI site of pHT01. The ligation mixture was transformed into DH5α competent cells. Positive clones were screened for a 1 ,188 bp PCR product by PCR amplification with primers T-groEL and B-NvB. s. (Spel BamHI). The positive clone was named pHT01 -HvC(B. s). Plasmid pHT01 -HvC(B. s) was used as a template for PCR amplification of the PgroE-ilvC fused fragment.
Plasmid pBD64 (Minton et al., Nucleic Acids Res. 18:1651 (1990)) is a fairly stable vector for expression of foreign genes in B. subtilis and contains a repB gene and chloramphenicol and kanamycin resistance genes for selection in B. subtilis. This plasmid was used for expression of HvC and bdhB under the control of a PgroE promoter. To clone PgroE-ilvC, bdhB and a lacl repressor gene into plasmid pBD64, a one-step assembly method was used (Tsuge et al., Nucleic Acids Res. 31 :e133 (2003)). A 3,588 bp pBD64 fragment containing a repB gene, which included the replication function, and the kanamycin antibiotic marker was PCR- amplified from pBD64 with primers T-BD64(Dralll) (SEQ ID NO:152), which introduced a Dralll sequence (CACCGAGTG), and B-BD64(Dralll) (SEQ ID NO:153), which introduced a Dralll sequence (CACCTGGTG). A 1 ,327 bp lacl repressor gene was PCR-amplified from pMUTIN4 (Vagner et al., Microbiol. 144:3097-3104 (1998)) with T-laclq(Dralll) (SEQ ID NO:154), which introduced a Dralll sequence (CACCAGGTG) and B- laclq(Dralll) (SEQ ID NO:155), which introduced a Dralll sequence (CACGGGGTG). A 1 ,224 bp PgroE-/7vC fused cassette was PCR- amplified from pHT01 -ilvC(B.s) with T-groE(Dralll) (SEQ ID NO:156), which introduced a Dralll sequence (CACCCCGTG), and B- B.s.ilvC(Dralll) (SEQ ID NO:157), which introduced a Dralll sequence (CACCGIGTG). A 1.2 kbp bdhB gene (SEQ ID NO:158) was PCR- amplified from Clostridium acetobutylicum (ATCC 824) genomic DNA with primers T-bdhB(Dralll) (SEQ ID NO:159), which introduced a Dralll sequence (CACACGGTG), and B-bdhB(rrnBT1 Dralll) (SEQ ID NO:160), which introduced a Dralll sequence (CACTCGGTG). The three underlined letters in the variable region of the Dralll recognition sequences were designed for specific base-pairing to assemble the four fragments with an order of pBD64-/ac/-PgroE/Vi/C-ιbc//7β. Each PCR product with Dralll sites at both ends was digested separately with Dralll, and the resulting Dralll fragments, 3,588 bp pBD64, lacl, PgroE/Vi/C, and bdhB were gel-purified using a QIAGEN gel extraction kit (QIAGEN). A mixture containing an equimolar concentration of each fragment with a total DNA concentration of 30 to 50 μg /100 μl_ was prepared for ligation. The ligation solution was then incubated at 16 0C overnight. The ligation generated high molecular weight tandem repeat DNA. The ligated long, linear DNA mixture was directly transformed into competent B. subtilis BE1010, prepared as described above. B. subtilis preferentially takes up long repeated linear DNA forms, rather than circular DNA to establish a plasmid. After transformation the culture was spread onto an LB plate containing 10 μg/mL of kanamycin for selection. Positive recombinant plasmids were screened by Dralll digestion, giving four fragments with an expected size of 3,588 bp (pBD64), 1 ,327 bp {lad), 1 ,224 bp (PgorE-//i/C), and 1 ,194 bp (bdhB). The positive plasmid was named pBDPgroE-ilvC(B.s.)-bdhB.
Demonstration of isobutanol production from glucose or sucrose by B. subtilis BE1010 ΔsacB::PqroE-budB-ilvD-kivD/pBDPqroE-ilvC(B.s.)- bdhB. To construct the recombinant B. subtilis expressing the five genes of the isobutanol biosynthetic pathway, competent cells of the two integrants B. subtilis BE1010 ΔsacB-PgroE-budB-ilvD-kivD #1 -7 and B. subtilis BE1010 ΔsacB::PgroE-budB-ilvD-kivD #8-16 were prepared as described above, and transformed with plasmid pBDPgroE-ilvC(B.s.)- bdhB, yielding B. subtilis BE1010 ΔsacB::PgroE-budB-ilvD-kivD #1-
7/pBDPgroE-ilvC(B.s.)-bdhB and B. subtilis BE1010 ΔsacB::PgroE-budB- ilvD-kivD #8-16/pBDPgroE-ilvC(B.s.)-bdhB.
The two recombinant strains were inoculated in either 25 ml_ or 100 ml_ of glucose medium containing kanamycin (10 μg /ml_) in 125 ml_ flasks to simulate high and low oxygen conditions, respectively, and aerobically grown at 37 0C with shaking at 200 rpm. The medium consisted of 10 mM (NhU)2SO4, 5 mM potassium phosphate buffer (pH 7.0), 100 mM MOPS/KOH buffer (pH 7.0), 20 mM glutamic acid/KOH (pH 7.0), 2% S10 metal mix, 1 % glucose, 0.01 % yeast extract, 0.01 % casamino acids, and 50 μg/mL each of L-tryptophan, L-methionine, and L-lysine. The S10 metal mix consisted of 200 mM MgCI2, 70 mM CaCI2, 5 mM MnCI2, 0.1 mM FeCI3, 0.1 mM ZnCI2, 0.2 mM thiamine hydrochloride, 0.172 mM CuSO4, 0.253 mM CoCI2, and 0.242 mM Na2MoO4. The cells were induced with 1.0 mM isopropyl-β-D-thiogalactopyranoiside (IPTG) at early-log phase (OD600 of approximately 0.2). At 24 h after inoculation, an aliquot of the broth was analyzed by HPLC (Shodex Sugar SH1011 column) with refractive index (Rl) detection for isobutanol content, as described in the General Methods section. The HPLC results are shown in Table 20.
Table 20
Production of Isobutanol from Glucose by B. subtilis BE1010 ΔsacB::PqroE-budB-ilvD-kivD/pBDPqroE-ilvC(B.s.)-bdhB Strains
Figure imgf000107_0001
B. subtilis a is B. subtilis BE1010 ΔsacB::PgroE-budB-ilvD-kivD #1-7/ pBDPgroE-ilvC(B.s.)-bdhB β. subtilis b is B. subtilis BE1010 ΔsacB::PgroE-budB-ilvD-kivD #8-16/ pBDPgroE-ilvC(B.s.)-bdhB
The isolate of B. subtilis BE1010 ΔsacB::PgroE-budB-ilvD-kivD #1-
7/pBDPgroE-ilvC(B.s.)-bdhB was also examined for isobutanol production from sucrose, essentially as described above. The recombinant strain was inoculated in 25 mL or 75 mL of sucrose medium containing kanamycin (10 μg /mL) in 125 mL flasks to simulate high and medium oxygen levels, and grown at 37 0C with shaking at 200 rpm. The sucrose medium was identical to the glucose medium except that glucose (10 g/L) was replaced with 10 g/L of sucrose. The cells were uninduced, or induced with 1.0 mM isopropyl-β-D-thiogalactopyranoiside (IPTG) at early-log phase (OD600 of approximately 0.2). At 24 h after inoculation, an aliquot of the broth was analyzed by HPLC (Shodex Sugar SH1011 column) with refractive index (Rl) detection for isobutanol content, as described in the General Methods section. The HPLC results are given in Table 21. Table 21
Production of lsobutanol from Sucrose by B. subtilis Strain BE1010 ΔsacB::PqroE-budB-ilvD-kivD/pBDPqroE-ilvC(B.s.)-bdhB
Figure imgf000108_0001
B. subtilis a is B. subtilis BE1010 ΔsacB::PgroE-budB-ilvD-kivD #1-7/ pBDPgroE-ilvC(B.s.)-bdhB
EXAMPLE 25 (Prophetic) Expression of an Isobutanol Biosynthetic Pathway in Lactobacillus plantarum
The purpose of this prophetic Example is to describe how to express an isobutanol biosynthetic pathway in Lactobacillus plantarum. The five genes of the isobutanol pathway, encoding five enzyme activities, are divided into two operons for expression. The budB, HvD and kivD genes, encoding the enzymes acetolactate synthase, acetohydroxy acid dehydratase, and branched-chain α-keto acid decarboxylase, respectively, are integrated into the chromosome of Lactobacillus plantarum by homologous recombination using the method described by Hols et al. {Appl. Environ. Microbiol. 60:1401-1413 (1994)). The remaining two genes (HvC and bdhB, encoding the enzymes acetohydroxy acid reductoisomerase and butanol dehydrogenase, respectively) are cloned into an expression plasmid and transformed into the Lactobacillus strain carrying the integrated isobutanol genes. Lactobacillus plantarum is grown in MRS medium (Difco Laboratories, Detroit, Ml) at 370C, and chromosomal DNA is isolated as described by Moreira et al. (BMC Microbiol. 5:15 (2005)).
Integration. The budB-ilvD-kivD cassette under the control of the synthetic P11 promoter (Rud et al., Microbiology 152:1011 -1019 (2006)) is integrated into the chromosome of Lactobacillus plantarum ATCC BAA- 793 (NCIMB 8826) at the IdhLI locus by homologous recombination. To build the IdhL integration targeting vector, a DNA fragment from Lactobacillus plantarum (Genbank NC_004567) with homology to IdhL is PCR amplified with primers LDH EcoRV F (SEQ ID NO:161 ) and LDH AatllR (SEQ ID NO:162). The 1986 bp PCR fragment is cloned into pCR4Blunt-TOPO and sequenced. The pCR4Blunt-TOPO-ldhL1 clone is digested with EcoRV and Aatll releasing a 1982 bp IdhLI fragment that is gel-purified. The integration vector pFP988, given as SEQ ID NO:177, is digested with Hindlll and treated with Klenow DNA polymerase to blunt the ends. The linearized plasmid is then digested with Aatll and the 2931 bp vector fragment is gel purified. The EcoRV/Aatll IdhLI fragment is ligated with the pFP988 vector fragment and transformed into E. coli Top10 cells. Transformants are selected on LB agar plates containing ampicillin (100 μg/mL) and are screened by colony PCR to confirm construction of pFP988-ldhL.
To add a selectable marker to the integrating DNA, the Cm gene with its promoter is PCR amplified from pC194 (GenBank NC_002013, SEQ ID NO:267) with primers Cm F (SEQ ID NO:163) and Cm R (SEQ ID NO:164), amplifying a 836 bp PCR product. This PCR product is cloned into pCR4Blunt-TOPO and transformed into E. coli Top10 cells, creating pCR4Blunt-TOPO-Cm. After sequencing to confirm that no errors are introduced by PCR, the Cm cassette is digested from pCR4Blunt-TOPO- Cm as an 828 bp Mlul/Swal fragment and is gel purified. The IdhL- homology containing integration vector pFP988-ldhL is digested with MIuI and Swal and the 4740 bp vector fragment is gel purified. The Cm cassette fragment is ligated with the pFP988-ldhL vector creating pFP988- DldhL::Cm.
Finally the budB-ilvD-kivD cassette from pFP988DssPspac-budB- ilvD-kivD, described in Example 24, is modified to replace the amylase promoter with the synthetic P11 promoter. Then, the whole operon is moved into pFP988-DldhL::Cm. The P11 promoter is built by oligonucleotide annealing with primer P11 F-Stul (SEQ ID NO:165) and P11 R-Spel (SEQ ID NO:166). The annealed oligonucleotide is gel- purified on a 6% Ultra PAGE gel (Embi Tec, San Diego, CA). The plasmid pFP988DssPspac-budB-ilvD-kivD, containing the amylase promoter, is digested with Stul and Spel and the resulting 10.9 kbp vector fragment is gel-purified. The isolated P11 fragment is ligated with the digested pFP988DssPspac-budB-ilvD-kivD to create pFP988-P11 -budB-ilvD-kivD. Plasmid pFP988-P11 -budB-ilvD-kivD is then digested with Stul and BamHI and the resulting 5.4 kbp P11 -budB-ilvD-kivD fragment is gel- purified. pFP988-DldhL::Cm is digested with Hpal and BamHI and the 5.5 kbp vector fragment isolated. The budB-ilvD-kivD operon is ligated with the integration vector pFP988-Dldhl_::Cm to create pFP988-Dldhl_-P11 - budB-ilvD-kivD::Cm.
Integration of pFP988-DldhL-P11 -budB-ilvD-kivD::Cm into L. plantarum BAA-793 to form L. plantarum ΔldhL.1 ::budB-ilvD-kivD::Cm comprising exogenous budB, HvD, and kivD genes. Electrocompetent cells of L. plantarum are prepared as described by Aukrust, T.W., et al. (In: Electroporation Protocols for Microorganisms; Nickoloff, J. A., Ed.; Methods in Molecular Biology, Vol. 47; Humana Press, Inc., Totowa, NJ, 1995, pp 201 -208). After electroporation, cells are outgrown in MRSSM medium (MRS medium supplemented with 0.5 M sucrose and 0.1 M MgCl2) as described by Aukrust et al. supra for 2 h at 370C without shaking. Electroporated cells are plated for selection on MRS plates containing chloramphenicol (10 μg/mL) and incubated at 370C. Transformants are initially screened by colony PCR amplification to confirm integration, and initial positive clones are then more rigorously screened by PCR amplification with a battery of primers.
Plasmid Expression of HvC and bdhB genes. The remaining two isobutanol genes are expressed from plasmid pTRKH3 (O'Sullivan DJ and Klaenhammer TR, Gene 137:227-231 (1993)) under the control of the L plantarum IdhL promoter (Ferain et al., J. Bacteriol. 176:596-601 (1994)). The IdhL promoter is PCR amplified from the genome of L. plantarum ATCC BAA-793 using primers PldhL F-Hindlll (SEQ ID NO:167) and PldhL R-BamHI (SEQ ID NO:168). The 411 bp PCR product is cloned into pCR4Blunt-TOPO and sequenced. The resulting plasmid, pCR4Blunt- TOPO-PIdhL is digested with Hindlll and BamHI releasing the PldhL fragment.
Plasmid pTRKH3 is digested with Hindlll and Sphl and the gel- purified vector fragment is ligated with the PldhL fragment and the gel- purified 2.4 kbp BamHI/Sphl fragment containing ilvC(B.s.)-bdhB from the Bacillus expression plasmid pBDPgroE-ilvC(B.s.)-bdhB (Example 24) in a three-way ligation. The ligation mixture is transformed into E. coli Top 10 cells and transformants are grown on Brain Heart Infusion (BHI, Difco Laboratories, Detroit, Ml) plates containing erythromycin (150 mg/L). Transformants are screened by PCR to confirm construction. The resulting expression plasmid, pTRKH3-ilvC(B.s.)-bdhB is transformed into L. plantarum ΔldhLI ::budB-ilvD-kivD::Cm by electroporation, as described above.
L. plantarum ΔldhLI ::budB-ilvD-kivD::Cm containing pTRKH3- ilvC(B.s.)-bdhB is inoculated into a 250 mL shake flask containing 50 mL of MRS medium plus erythromycin (10 μg/mL) and grown at 37 0C for 18 to 24 h without shaking, after which isobutanol is detected by HPLC or GC analysis, as described in the General Methods section.
EXAMPLE 26 (Prophetic) Expression of an Isobutanol Biosynthetic Pathway in
Enterococcus faecalis
The purpose of this prophetic Example is to describe how to express an isobutanol biosynthetic pathway in Enterococcus faecalis. The complete genome sequence of Enterococcus faecalis strain V583, which is used as the host strain for the expression of the isobutanol biosynthetic pathway in this Example, has been published (Paulsen et al., Science 299:2071 -2074 (2003)). An E. co///Gram-positive shuttle vector, Plasmid pTRKH3 (O'Sullivan DJ and Klaenhammer TR, Gene 137:227-231 (1993)), is used for expression of the five genes (budB, HvC, HvD, kivD, bdhB) of the isobutanol pathway in one operon. pTRKH3 contains an E. coli plasmid p15A replication origin, the pAMβi replicon, and two antibiotic resistance selection markers for tetracycline and erythromycin. Tetracycline resistance is only expressed in E. coli, and erythromycin resistance is expressed in both E. coli and Gram-positive bacteria. Plasmid pAMβi derivatives can replicate in E. faecalis (Poyart et al., FEMS Microbiol. Lett. 156:193-198 (1997)). The inducible nisA promoter (PnisA), which has been used for efficient control of gene expression by nisin in a variety of Gram-positive bacteria including Enterococcus faecalis (Eichenbaum et al., Appl. Environ. Microbiol. 64:2763-2769 (1998)), is used to control expression of the five desired genes encoding the enzymes of the isobutanol biosynthetic pathway.
The plasmid pTrc99A::budB-ilvC-ilvD-kivD (described in Example 18), which contains the isobutanol pathway operon, is modified to replace the E. coli HvC gene (SEQ ID NO:3) with the B. subtilis HvC gene (SEQ ID NO:184). Additionally, the bdhB gene(SEQ ID NO:158) from Clostridium acetobutylicum is added to the end of the operon. First, the bdhB gene from pBDPgroE-ilvC(B.s.)-bdhB (described in Example 24) is amplified using primers F-bdhB-Avrll (SEQ ID NO:169) and R-bdhB-BamHI (SEQ ID NO:170), and then TOPO cloned and sequenced. The 1194 bp bdhB fragment is isolated by digestion with Avrll and BamHI, followed by gel purification. This bdhB fragment is ligated with pTrc99A::budB-ilvC-ilvD- kivD that has previously been digested with Avrll and BamHI and the resulting fragment is gel purified. The ligation mixture is transformed into E. coli Top10 cells by electroporation and transformants are selected following overnight growth at 37 0C on LB agar plates containing ampicillin (100 μg/mL). The transformants are then screened by colony PCR to confirm the correct clone containing pTrc99A::budB-ilvC-ilvD-kivD-bdhB. Next, /VvC(B.s.) is amplified from pBDPgroE-ilvC(B.s.)-bdhB
(described in Example 24) using primers F-HvC(B. s.)-Aflll (SEQ ID NO:171 ) and R-ilvC(B.s.)-Notl (SEQ ID NO:172). The PCR product is TOPO cloned and sequenced. The 1051 bp HvC(B.s.) fragment is isolated by digestion with AfIII and Notl followed by gel purification. This fragment is ligated with pTrc99A::budB-ilvC-ilvD-kivD-bdhB that has been cut with AfIII and Notl to release the E. coli HvC (the 10.7 kbp vector band is gel purified prior to ligation with HvC(B. s.)). The ligation mixture is transformed into E. coli Top10 cells by electroporation and transformants are selected following overnight growth at 37 0C on LB agar plates containing ampicillin (100 μg/mL). The transformants are then screened by colony PCR to confirm the correct clone containing pTrc99A::budB-ilvC(B.s.)-ilvD-kivD- bdhB. To provide a promoter for the E. colil Gram-positive shuttle vector pTRKH3, the nisA promoter (Chandrapati et al., MoI. Microbiol. 46(2):467- 477 (2002)) is PCR-amplified from Lactococcus lactis genomic DNA with primers F-PnisA(Hindlll) (SEQ ID NO:173) and R-PnisA(Spel BamHI) (SEQ ID NO:174) and then TOPO cloned. After sequencing, the 213 bp nisA promoter fragment is isolated by digestion with Hindlll and BamHI followed by gel purification. Plasmid pTRKH3 is digested with Hindlll and BamHI and the vector fragment is gel-purified. The linearized pTRKH3 is ligated with the PnisA fragment and transformed into E. coli Top10 cells by electroporation. Transformants are selected following overnight growth at 37 0C on LB agar plates containing erythromycin (25 μg/mL). The transformants are then screened by colony PCR to confirm the correct clone of pTRKH3-PnisA.
Plasmid pTRKH3-PnisA is digested with Spel and BamHI, and the vector is gel-purified. Plasmid pTrc99A::budB-ilvC(B.s)-ilvD-kivD-bdhB, described above, is digested with Spel and BamHI, and the 7.5 kbp fragment is gel-purified. The 7.5 kbp budB-ilvC(B.s)-ilvD-kivD-bdhB fragment is ligated into the pTRKH3-PnisA vector at the Spel and BamHI sites. The ligation mixture is transformed into E. coli Top10 cells by electroporation and transformants are selected following overnight growth on LB agar plates containing erythromycin (25 μg/mL) at 37 0C. The transformants are then screened by colony PCR. The resulting plasmid is named pTRKH3-PnisA-budB-ilvC(B.s)-ilvD-kivD-bdhB. This plasmid is prepared from the E. coli transformants and transformed into electro- competent E. faecalis V583 cells by electroporation using methods known in the art (Aukrust, T.W., et al. In: Electroporation Protocols for
Microorganisms; Nickoloff, J. A., Ed.; Methods in Molecular Biology, Vol. 47; Humana Press, Inc., Totowa, NJ., 1995, pp 217-226), resulting in E. faecalis V583/ pTRKH3-PnisA-budB-ilvC(B.s)-ilvD-kivD-bdhB. The second plasmid containing nisA regulatory genes, nisR and nisK, the add9 spectinomycin resistance gene, and the pSH71 origin of replication is transformed into E. faecalis V583/ pTRKH3-PnisA-budB- NvC(B. s)-ilvD-kivD-bdhB by electroporation. The plasmid containing pSH71 origin of replication is compatible with pAMβi derivatives in E. faecalis (Eichenbaum et al., supra). Double drug resistant transformants are selected on LB agar plates containing erythromycin (25 μg/mL) and spectinomycin (100 μg/mL), grown at 37 0C.
The resulting E. faecalis strain V583B harboring two plasmids, i.e., an expression plasmid (pTRKH3-PnisA-budB-ilvC(B.s)-ilvD-kivD-bdhB) and a regulatory plasmid (pSH71 -nisRK), is inoculated into a 250 mL shake flask containing 50 mL of Todd- Hewitt broth supplemented with yeast extract (0.2%) (Fischetti et al., J. Exp. Med. 161 :1384-1401 (1985)), nisin (20 μg/mL) (Eichenbaum et al., supra), erythromycin (25 μg/mL), and spectinomycin (100 μg/mL). The flask is incubated without shaking at 37 0C for 18-24 h, after which time, isobutanol production is measured by HPLC or GC analysis, as described in the General Methods section.
EXAMPLE 27 Increased tolerance of Saccharomvces cerevisiae to isobutanol at decreased growth temperatures
Tolerance levels were determined for yeast strain Saccharomyces cerevisiae BY4741 (ATCC 201388) at 25 0C and 30 0C as follows. The strain was cultured in YPD medium. Overnight cultures in the absence of any test compound were started in 25 mL of YPD medium in 150 mL flasks with incubation at 30 0C or at 25 0C in shaking water baths. The next morning, each overnight culture was diluted into a 500 mL flask containing 300 mL of fresh medium to an initial OD600 of about 0.1. The flasks were incubated in shaking water baths at 30 0C or 25 °, using the same temperature as used for each overnight culture. The large cultures were incubated for 3 hours and then were split into flasks in the absence (control) and in the presence of 2% or 3% of isobutanol. Growth was followed by measuring OD600 for six hours after addition of the isobutanol. The ΔOD6oo was calculated by subtracting the initial OD6oo from the final OD6Oo at 6 hours. The percent growth inhibition relative to the control culture was calculated as follows: % Growth Inhibition = 100 - [100(Sample ΔOD6oo/Control ΔOD6oo)]- The results are summarized in Table 22 below and indicate that growth of strain BY4741 is less inhibited by 2% isobutanol at 25 0C than by 2% isobutanol at 30 0C.
Table 22. Growth of Saccharomyces cerevisiae Strain BY4741 at 25 0C and 30 0C with Isobutanol.
% % Growth
Isobutanol Temperature Inhibition
2 30 99
2 25 84
3 30 No growth
3 25 No growth

Claims

CLAIMSWhat is claimed is:
1. A method for the production of isobutanol comprising: a) providing a recombinant microbial production host which produces isobutanol; b) seeding the production host of (a) into a fermentation medium comprising a fermentable carbon substrate to create a fermentation culture; c) growing the production host in the fermentation culture at a first temperature for a first period of time; d) lowering the temperature of the fermentation culture to a second temperature; and e) incubating the production host at the second temperature of step (d) for a second period of time; whereby isobutanol is produced.
2. A method according to Claim 1 wherein the fermentable carbon substrate is derived from a grain or sugar source selected from the group consisting of wheat, corn, barley, oats, rye, sugar cane, sugar beets, cassava, sweet sorghum, and mixtures thereof.
3. A method according to Claim 1 wherein the fermentable carbon substrate is derived from cellulosic or lignocellulosic biomass selected from the group consisting of corn cobs, crop residues, corn husks, corn stover, grasses, wheat straw, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, soy, components obtained from milling of grains, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof.
4. A method according to Claim 1 wherein the fermentable carbon substrate is selected from the group consisting of monosaccharides, oligosaccharides, and polysaccharides.
5. A method according to Claim 1 wherein the fermentation culture is maintained under conditions selected from the group consisting of anaerobic conditions and microaerobic conditions.
6. A method according to Claim 1 wherein while growing the production host in (c) at a first temperature over a first period of time, a metabolic parameter of the fermentation culture is monitored.
7. A method according to Claim 6 wherein the metabolic parameter that is monitored is selected from the group consisting of optical density, pH, respiratory quotient, fermentable carbon substrate utilization, CO2 production, and isobutanol production.
8 A method according to Claim 1 wherein lowering the temperature of the fermentation culture of step (d) occurs at a predetermined time.
9. A method according to Claim 1 wherein the lowering of the temperature of the fermentation culture of step (d) coincides with a change in a metabolic parameter.
10 A method according to Claim 9 wherein the change in metabolic parameter is a decrease in the rate of isobutanol production.
11. A method according to Claim 1 wherein the first temperature is from about 25 0C to about 40 0C.
12. A method according to Claim 1 wherein the second temperature is from about 3 0C to about 25 0C lower than the first temperature.
13. A method according to Claim 1 wherein steps (d) and (e) are repeated one or more times.
14. A method according to Claim 1 wherein the recombinant microbial production host is selected from the group consisting of Clostridium, Zymomonas, Escherichia, Salmonella, Rhodococcus, Pseudomonas, Bacillus, Lactobacillus, Enterococcus, Alcaligenes, Klebsiella, Paenibacillus, Arthrobacter, Corynebacterium, Brevibacterium, Saccharomyces, and Pichia.
15. A method according to Claim 1 wherein the recombinant microbial host cell comprises at least one DNA molecule encoding a polypeptide that catalyzes a substrate to product conversion selected from the group consisting of: a) pyruvate to acetolactate; b) acetolactate to 2,3-dihydroxyisovalerate; c) 2,3-dihydroxyisovalerate to α-ketoisovalerate; d) α-ketoisovalerate to isobutyraldehyde; and e) isobutyraldehyde to isobutanol; wherein the at least one DNA molecule is heterologous to said microbial production host cell.
16. A method according to Claim 15 wherein the polypeptide that catalyzes a substrate to product conversion of pyruvate to acetolactate is acetolactate synthase.
17. A method according to Claim 15 wherein the polypeptide that catalyzes a substrate to product conversion of acetolactate to 2,3- dihydroxyisovalerate is acetohydroxy acid isomeroreductase.
18. A method according to Claim 15 wherein the polypeptide that catalyzes a substrate to product conversion of of 2,3-dihydroxyisovalerate to α-ketoisovalerate is acetohydroxy acid dehydratase.
19. A method according to Claim 15 wherein the polypeptide that catalyzes a substrate to product conversion of α-ketoisovalerate to isobutyraldehyde is branched-chain α-keto acid decarboxylase.
20. A method according to Claim 15 wherein the polypeptide that catalyzes a substrate to product conversion of isobutyraldehyde to isobutanol is branched-chain alcohol dehydrogenase.
21. A method according to Claim 16 wherein the acetolactate synthase has an amino acid sequence having at least 95% identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:178, and SEQ ID NO:180, based on the Clustal W method of alignment using the default parameters of GAP PENALTY=I O, GAP LENGTH PENALTY=O.1 , and Gonnet 250 series of protein weight matrix.
22. A method according to Claim 17 wherein the acetohydroxy acid isomeroreductase has an amino acid sequence having at least 95% identity to an amino acid sequence selected from the group consisting of SEQ ID NO:43, SEQ ID NO:181 , SEQ ID NO:183, and SEQ ID NO:185, based on the Clustal W method of alignment using the default parameters Of GAP PENALTY=I O, GAP LENGTH PENALTY=O.1 , and Gonnet 250 series of protein weight matrix.
23. A method according to Claim 18 wherein the acetohydroxy acid dehydratase has an amino acid sequence having at least 95% identity to an amino acid sequence selected from the group consisting of SEQ ID NO:6, SEQ ID NO:186, SEQ ID NO:188, and SEQ ID NO:190, based on the Clustal W method of alignment using the default parameters of GAP PENALTY=I 0, GAP LENGTH PENALTY=O.1 , and Gonnet 250 series of protein weight matrix.
24. A method according to Claim 19 wherein the branched-chain α-keto acid decarboxylase has an amino acid sequence having at least 95% identity to an amino acid sequence selected from the group consisting of SEQ ID NO:8, SEQ ID NO:193, SEQ ID NO:195, and SEQ ID NO:197, based on the Clustal W method of alignment using the default parameters of GAP PENALTY=IO, GAP LENGTH PENALTY=O.1 , and Gonnet 250 series of protein weight matrix.
25. A method according to Claim 20 wherein the branched-chain alcohol dehydrogenase has an amino acid sequence having at least 95% identity to an amino acid sequence selected from the group consisting of SEQ ID NO:10, SEQ ID NO:199, SEQ ID NO:201 , SEQ ID NO:203, and SEQ ID NO:204, based on the Clustal W method of alignment using the default parameters of GAP PENALTY=IO, GAP LENGTH PENALTY=O-I , and Gonnet 250 series of protein weight matrix.
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